Well, Sonar will give you the 32/64 install option, and you will also get the chance to override the location of the 64-bit plugins.
As far as where either 32-bit or 64-bit plugins are located, Sonar will launch with a default set of paths that includes the one you chose for the install. Once it is up and running, you can launch the Cakewalk Plugin Manager and add whatever additional path(s) you wish.
I DO recommend leaving your setup so that you can launch EITHER 32-bit or 64-bit Sonar, in case you have projects that just do not like having certain 32-bit plugins present in 64-bit Sonar. (This is a frequent source of much drama and anguish).
In addition, I suggest you individually test out the viability of each 32-bit plugin to work in 64-bit Sonar (for which there is not a 64-bit replacement), and create a sub-folder within your 32-bit plugin folder and move the 32-bit plugins that work in 64-bit Sonar to the sub-folder. THEN, you can add only the sub-folder with the tested plugins that work in 64-bit Sonar to the search path for 64-bit Sonar, and voila, you will be good to go.
Doing the above will preserve the availability of all of your 32-bit plugins in your 32-bit Sonar, because the search in the 32-bit Sonar will automatically pick up the contents of the new sub-folder.
I HOPE any and all of the above makes sense, and wish you the best of it all.
Bob Bone