if wall of text is imtimidating go to last paragraph as its the TL;DR version.
The lore ive written up would make sense to how they could be integrated (its prettyu damn long and is an extremely rough draft):
The wolf-race is a very intellegent species of sentient creatures originating from Atmora. Due to there naturally bestowed gifts of fur claw smell and night vision, they advanced faster then the nords in evolution, basicly always being a step ahead of man in technology and magic allowing them to have stayed hidden from man kind for centuries. The wolf race avoided man because of how advanced they were to him, the wolf race was afraid of war that the humans seemed to love to always have.
Long before the civil war that forced Ysgramor and other Nords to migrate to skyrim, the wolf race had there own civil war between the 2 most powerful "packs" which resembled modern day city states but on a grander scale. After much war the 2 packs ended up signing peace treaties and forming one alliance and a reign of peace unlike any seen before befell the wolf race. centuries passed before the first human visited them who was capable of getting past the wolf races magic ward which hid the mega city state that the wolves called their home. This man was the leader of a group of mages who were trying to escape the civil war that had now fallen onto Atmora. At first the humans were welcomed with open arms, as most of the wolf race had never seen the mythical human being before in their entire lives. But it did not last, some within the group leading the wolves felt that the presence of humans in their grand city could lead to even more humans coming which could then lead to a catostrophic war that the ancestors of the wolves had tried so hard to avoid while others felt that the introduction of other intelligent species was inevitable and has opened the door to many great things. This lead to a split in the leaders regarding the humans. after weeks of debate, some on the side that felt that the humans were a threat needed to "disapear". Now the mage who brought over many other mages had also brought over refugees from the war torn cities of Atmora. The Oposition wolves started kidnapping humans one at a time. it wasnt long before the great mage discovered what was happenning, so he met with the "Alpha" or king to try and get to the bottom of what was going on. The Alpha knew very little about the in fightings of his trusted cabnit regarding humans, as far as she was concerned, the humans were purely nuetral and didnt pose any threat, so when the mage came to the Alpha infuriated at what had happened, both started argueing with one another until that escalated into a fight, but before the first blow could be done, the Mage cast an extremely powerful curse on the mega city, which would make the wolf race become what they truely were, monsters. shortly after the Mage was struck down by the main opposer of the humans. (whos name i cant think of as this entire Lore is a rough draft) The Alpha asked what was going on and the opposer said that the humans had started attacking the people! Little did the alpha know that the anti humanists had attacked the humans which started the battle between the mages and the wolves. At the end of the battle all but one human was slain, a little girl who had escaped. After regrouping, the Alpha nad the council discussed what was to happen, with the anti humanists screaming that they were right all along, but there was opposition in the pro humanists that the entire thing was staged and all of this was caused by the anti humanists, which led to more debate with no one going anywere. Now the curse that was cast set in the full moon of that night. Everyone in the city became a werewolf, disrupting their minds and causing blood lust in everyone. Chaos accross the city, the Alpha who had always had major power of mind over matter was fighting the changes and bloodlust as much as she could, but she couldnt prevent the inevitable and escaped the city transforming into a werewolf were she laid chase to a human, before killing the child she gained control of herself enough to back from the child and contrain herself, and ran away from the child. the next morning the city was in ruins, masses of people were missing and wolves killed by other wolves in pure blood lust litered the street. The Alpha awoke in the forest were the little girl had followed the werewolf alpha keeping her distance. The Alpha knowing she was there called for her and asked what had happened. She told how the wolves came and started attacking her parents and tried killing all the humans when the mages started fighting back. This Alpha coming back to the city naked went straight for the main oppser and killed him outright on the spot, following the execution of the remaining anti humanists in the Alpha's cabinet. From then on out the wolf race started to dwindle in numbers to the point were the mega city that was once the crown jewl of the wolf race was mostly a ghost city. Extinction on the horizon, the mages of the wolves tried everything to prevent further bloodlust and death in changing. The only soltuion that could be found was the use of silver shackles on each citizen when they went to sleep. it was not for another century when a way to prevent bloodlust was found, and not too long after a cure was found for their lycanthropy, but it had come very late as the city was almost completely in ruins, the wilderness around the city was devasted and barren of game from werewolves rauaging the country side. Overall the population of the Wolf Race had dwindled to a mere 30% of what it once was, and because of having to allocate all resources in finding a cure the wolves ended up being on par with the humans in terms of technology and magic. The Alpha at the time declared that it would be within there best interestests if they finally were to move out of isolation and integrated into the world. with little to no arguemant in nay say, people gathered to dock onto the wolves great ships constructed solely for imigrating to new lands, the first in which they found was skyrim were they encountered other humans and the imperium. Having little support of the humans, the wolves made easy allies with the khajiit., which to this day is the only real ally the wolves have, but because of this on top of how scarce the wolves are at this point, humans view the wolves as if hey were khajiit holding major racial tension against them.
The wolves arrived 40 years before the events of skyrim, allowing them to have at least a small presence on skyrim before the player enters the game.
This is mega rough draft and is major TL;DR material, in a nutshell: Wolf race has been around for a long time and developed faster than humans, allowing for civilization to be set up when humans were still figuring things out. Wolves stay hidden from humans because of humans tendency for war. Wolves have civil war a long time before the civil war in Atmora, leading to peace lasting for a very long time. Peace ends when powerful magic user comes to wolves with refugees and other mages fleeing civil war in Atmora and since not all wolves like humans try to kill the humans. The powerful mage ends up cursing the entire mega city were the wolves reside with a very powerful curse of lycanthopy. All but 1 human is killed, first night of curse the Alpha or king of wolves finds human next day were the human tells the Alpha what happened, so the Alpha kills the people who started killing the humans. Slowly the wolves start deminishing and use silver to bind at night so as to not go and cause as much mayhem, but barely works. Cure is finally found many years later but after 70% of population dwindled, the city is mostly destroyed and the wilderness outside it is ravaged from werewolves killing all the game. Wolves only option is to expand out to the world and no longer stay in isolation. Send out mass ships of people with diplomats out to imigrate to new land, find skyrim and set presence there, not very well liked with humans, makes ally with khajiit. Wolves land 40 years before events of skyrim, allowing for presence of wolves to be known as well as make sense as to why one would be getting hauled off for execution hence another beast race in the elder scrolls.
What do ya guys think?