OP, have you considered going with a VM for tuning? That's what I do. Win XP in VMware w/ all my tuning software. Works great and it's portable on any PC I want it on.
You can use both application suites, however, the checksums are calculated differently with WinOLS vs. TunerPro via MTX. Make your changes in either application, but I'd recommend using TunerPro (MTX) to do the checksum as a final step on all bins. If you're just using WinOLS by itself, then it's fine for calculating checksums. The problem is if your bin was last modified by TunerPro, you must import it into your WinOLS project. At this point WinOLS no longer calcs the checksums properly. It can create quite the headache.
Can't say I agree... I always give WinOLS the last word in checksum calculation... It has never bricked my ECU unlike the MTX plug in.