Yes, the "affinity trick" is automatic as of 1.01.
The Vista "issue" is no longer an issue. The original warnings may have had merit back when the game was in development, and in the very early days of its release, but with the service packs and patching that has occurred since then, there is no longer a disadvantage to playing on Vista compared to any other OS. In fact some benchmarking efforts on the official forums have shown that Vista may actually be the best system to play on (superior to both XP and W7). That is why all the in-game warnings about Vista compatibility have been removed with the latest patch.
The fact that you're running into slow downs with very busy maps most likely is a result of your hardware. Even very low end machines can run BS smoothly on very simple missions, but will suffer greatly as unit count goes up. So, with that in mind, post your PC's specs, your detail settings, the name of the mission in which you encounter problems, and the average FPS that you get in the mission. It should be easy enough to tell if your slowdowns are a simple consequence of hardware that's not quite up to the task, or if there's something else that's degrading performance. But, once again, as long as your Vista installation is current, it is very doubtful that this had anything to do with your OS.