Multiple VST folders isn't a problem (and is quite common, if you need to manage VST2 32 bit, VST2 64bit, VST3, etc). And some VSTs seem to want to install in their own preferred place. You just have to make sure that all those folders are included in the search path in Sonar.
"Also Platinum seemed to have installed into X3's folder" - how so? It's common for there to be a SONAR Platinum folder and a SONAR X3 Producer (or whatever) folder both within Program Files\Cakewalk. But if you're saying that you've somehow ended with just 1 folder for both, i.e. with SONARPLT.exe and SONARPDR.exe (for example) in the same folder, then yeah, that probably got installed wrongly and needs a clean start.
You've not made it clear whether you can't use plugins
at all, or whether you're just getting annoying pop-ups that you need to get rid of, or whether it's just certain plugins that are a problem. Give us some more information and there's probably more help we can offer.