There's two things you can do here. One, uninstall all of your Waves plug-ins and reset your plugins within Sonar (this will delete any saved settings in a session for some reason). Install Waves again, and watch for the installation directories. You will be asked where you want your 64-Bit plugins, your 32-bit plug-ins, AND where you want WaveShell to be installed. You want ONLY the 32-bit plugins to install in a directory Sonar will never find. However, the 64-Bit plugins and the WaveShell MUST exist in both VST locations for 64 and 32 bit plug-ins, don't ask me why. Then, rescan for the plug-ins in Sonar and you should be all set.
The other option is to simply find your 32-bit plugins (in a directory close to your 32-bit WaveShell), and either delete them or simply move them to a hidden place. Then, re-scan for your plugins, possibly resetting your plug-ins in Sonar, which, again, will delete saved settings in your projects.
To get around the lost Waves settings, I had to go to each and every plug-in and manually save the plug-in's setting, then recall each plug-in's setting after the full reset.
The bottom line was that you NEED the 32-bit WaveShell as well as the 64-bit, but you ONLY need the 64-Bit plugins, which are normally installed in a directory close to or next to the WaveShell. This, of course, can be pre-determined by you during the Waves install as I mentioned in the first option.
Hope this helps!!