You.
I'm assuming you. Vampires do not control the whole of the world. They may have small pockets of power, such as Skingrad, but there is no way that they could control everything else. It also seems to me that cases like this are exactly how it's portrayed. They aren't a group of Vampires, but merely a single vampire in power. most Vampires tend to stick to a ruin or tomb and live as a clan, ala Morrowind (Oblivion had the same system, only not well presented). Also, how do they know who a werewolf is? Werewolves don't immigrate (on purpose) during thier beast-like state. They spill over into a territory by accident, or decide to leave thier province as a normal Man or Mer. They don't exactly adhere to the borderline laws of the Empire.
In short; vampires don't have much power. Werewolves are hard to trace.
I would agree. The Order's only concern is to live their life in peace and stability as an individual. They don't have huge clans, but just seperate groups of people who are counted amongst the Order. I would speculate that there could be vampires in the High Council, but it's mere speculation. Most vampires from the Cyrodilic tribe lived with someone. Jakben lived with his butler and a nest of other vampires beneath his house. Seridur lived with his bodyguards and the other mortals. Lord Lovidicus lived with his servants and an orc maid. Janus Hassildor lived with his wife, before she was put into a coma. They each live as an individual, but otherwise will recognize other vampires. But they do have some control over something. Because they are told to look for political influence or just a normal influence. And the funny thing is, all these vampiric NPC's do have influence. Jakben was known as a night owl, but he had an "unblemished" history. Seridur was a "respected member of the community." Janus Hassildor was known as a reclusive man, but he was also known for his beneficial work to Skingrad and his duty as count. Lovidicus cared enough to keep his mouth shut about telling everyone he fell in love with an orc woman. He feared his status as a noblemen would drop because of emotional entanglements with servants. But he still broke a tenet and told the orc he was a vampire which resulted in his entrapment.
Influence=power.
BUT, the Vampires in Cyrodiil work together to weed out the newcomers, or get them to join the clan. Read this, and you'll see: http://uesp.net/wiki/Lore:Immortal_Blood
Newcomers would never join the Cyrodilic clan. Any savage vampire that does not come from the Cyrodiil tribe is to be killed off because they are not blessed by Clavicus Vile. Almost every province has a different vampire clan in it. Illiac Bay has nine tribes, Morrowind has three and Valenwood has four. Cyrodiil has only a single tribe because they are very competitive and ruthless against other vampires. Since they believe they squander the gift of vampirism. They are very cultured and civilized, but nevertheless they still are "monsters" by the perspective of society.
What you said is true, to an extent. They both have the same cause. They wipe out any intruders to Cyrodiil by influencing people to do the work for them. As I recall, their tenets said "Our Strength is not in numbers, but in skillful manipulation of society".
Think of it as two or three people playing a board game against an enemy. They move the pieces and pawns and finally bring about their victory in handling the pieces. Similar to what they do with society. I doubt they go around on a rampage, slicing up rival vampires. While not impossible, it's unlikely unless the vampire hunter is indeed a vampire himself. That would be the ultimate deception.