well i can't vouch on whether dual- vs single-core performance since mine runs fine on my 3800 x2, but...
in regard to helping keep the affinity setting i use an app called WinLauncher XP (can't remember where i got it, i believe i found it trolling an old Shogo forum) that you can setup profiles for. you detail what .exe to run, core(s) to run, process priority, and display options. then you name the profile and u can just load through WinLauncher and it applies the settings and minimizes.
works wonders on older games that dislike dual-core (KOTOR being an example), and it should
work on new ones.
in case anyone is wondering: in view takes ~6megs of mem and when it minimizes ~2megs.
hah! found it off of Major Geeks' site: