Hi!
Not sure what the issue is, could you be more clear?
I use PCSX2 stand-alone emulator, and then just use the import wizard as usual. I haven't come across any compatability issues at all. I can tinker with PCSX2 for per-game configuration if I want to do things like apply differing options, but to be honest I generally just crank up the resolution a bit and play as-is without any issues.
Are you having particular issues?