I guess that it all depends how much knowledge each group has of the other. For example: Werewolves might think that vampires can be stopped with running water. Vampires might think that werewolves cannot set foot on holy ground.
Now I know the talk of course puts werewolves below vampire on the power scale which I never really paid much attention if this issue does become unavoidable has anyone found a way to bring them on the same level or at least make it feel so that if you are doing crossover games that one set of characters doesn't feel left in the dust?
I think the main balance is that werewolves require less politics to stay alive. A vampire can't make trouble, or he will find himself staked in his sleep. This is less of a concern for werewolves.
Unfortunately, this is a hard difference in power to bring up when you are crossing the two. If the vampires are working at night, the werewolves are probably going to focus their work at night too.
I've also usually considered werewolves main strength to be an area where vamps are weak. Namely, dealing with 'spirits'. I think vamps can manipulate ghosts, they do a little magic, and outside of video related equipment they have little problem with technology. They really don't have a good way to deal with spirits, and werewolves are all about spirits.
Which makes it funny that werewolves are usually seen subjugated by vampires...