More cores is always better for running more instances, until a point. Ideally, you want a CPU core per game instance, so if you're running 4 copies of a game you ideally want a 4-core. A 6-core is likewise better than a 4-core, particularly if you are running more than 4 game instances.
Someone recently asked about comparing an Intel i7 (4-core with hyperthreading to trick Windows into thinking it's 8-core) to a 6-core AMD Phenom. I haven't seen relevant benchmarking and don't have a Phenom to compare with (while I do have i7 boxes). However, I would expect the 6-core Phenom to outperform the 4-core i7 in a multboxing scenario,
especially if playing more than 4 instances.
As far as where "Until a point" comes in, there will be diminishing returns as the number of cores outpaces the number of game instances. Most games don't heavily multithread -- they almost all "have multiple threads" but other than the main (game logic, rendering, etc) thread they will typically be idling. So that means that additional cores beyond 1 per instance will still somewhat help, but nowhere near as significantly.
And finally, yes ISBoxer will help you configure all of your CPU cores, until you pass 32 or so of them but that's a few years out