When you say "Audio Units Manager" are you talking about Logic's AU Manager, or some third party application? Is it the Granted Software one?
If so, my versions of Waves 5 work well with them both. All that the Granted AU Manager does is move the component files (ie the Waveshell) between two directories to enable or disable the plugins, it won't affect Waves crashing at all.
Without knowing what you did when things stopped working it's difficult to say, but it may well be a Waves installation, copy protection or authorisation issue, they can be notoriously odd behaving sometimes.
Incidentally, why do you need two Waveshells? I think Logic only supports one of Waves' Waveshells at a time, at least it did in Logic 5, not sure about later ones.
Not sure what else to suggest, really...