I know that the mages guild has been split into two parts Synod and the College Of Whispers.But one thing i'm not sure about is if they will be different since they are two mage guilds.Can someone please explain to me how they will be different or give me a link that says more about their differences?

We don't really know anything about it. Someone might be able to bring up lore and speculation but in the end we'll just have to wait

Those things were mentioned in the TES novel, and were supposed to have happened more than a century before the events of skyrim. They might have twelve mages guild splits now, or any number.

All that I personally know thus far is that the Synod is religious (though how much so, I do not know).

However, we can infer a variety of things.

1. No "Mages Guild" and "Necromancers" this time - by going for lore-based names such as the Synod and the College of Whispers, Bethesda is declaring shades of grey with magic this time, rather than the blatant black and white contrast we saw in oblivion between the Necromancers and the Mages Guild.

2. The name "The College of Whispers" implies secrets - indicating a slightly darker themed guild than the Synod. However, it is possible that the two guilds are equally dark, just in different ways. The religious Synod may be more restricting, more controlling, and have a creepy cult type of thing going on. The College of Whispers on the other hand, may be like the Mages Guild flavored with a bit of the Dark Brotherhood's malice, and add a touch of the Thieves Guild's subtleties.

3. It has been heavily rumored that Necromancy is half of the Conjuration tree now - IF this is true, I see it as unlikely that even one of the guilds outright outlaws it's practices.

This is only speculation but I`m guessing The College of Whispers will focus more on stealthy magic such as illusion while Synod is a straight-forward destruction nuke guild.

If you think on it, though, Necromancy was also about half of the "conjouration tree" in Oblvion. There were two key types of summons. Daedra and undead. I never touched the necromancy. Daedra make me happy, and I dislike the smell of rotting flesh.

I think he was speaking more literally since they said that skills have skill trees now...in Conjuration there would be one that focuses on living-ish things (Daedra, animals and such) and Necromancy (skeletons, ghosts, whatnot...)

We're in Skyrim, whatever guilds or organizations are sanctioned by the new or old Empire don't have to play a role in Skyrim. Our info is 160 years old...

There could be some sort of Skyrim exclusive Druid Guild that is very tribal in its ways of magic. They might even allow necromancy.

We simply don't know, there is a new novel comming which will be out a few months before Skyrim. Perhaps that one takes place during the same period as Skyrim, and then we can make an educated guess. But by then we probably already know much more about the factions.

Don't forget that Skyrim IS still in the Empire. The civil war is (at least partially) loyalists vs. rebels.