WHAT IS Best way to clean up vst bridging mess

I have C5, thinking of upgrading to C6.5 but I would like to organize my plug-ins which are all over the place it seems. I’ve been using jbridge as well as Steinberg’s bridge. Oh yeah, I’m using Win7, 64bit with Cubase 64bit. I occasionally get crashes or older files not loading and I think part of it is because I was haphazard in the way I bridged the 32bit VST plugins. Not fully understanding how jbridge captures 32bit files for conversions I have folders in several locations. It seems like plugins like those from NI want to be on the C drive

So if I upgrade, which I assume it will be a separate install - going from V5 to 6.5 - my question is: is there a way to pre-organize my vst plugins systematically and not screw up the songs I’ve been working on? Suggestions?