I think you're trying to solve two different issues at the same time:
1. solving how to copy your tags from AAC to WAV
2. solving how to have two libraries, one with lossless and one with lossy
I think your original question was about how to perform (1).
A MC "library" is an internal database that supports fast access, searching and organization for your files on disk. It also maintains many settings/options.
Your goal for (1) is to simply create a new library, importing only the AAC files (so that you can safely and easily swap out the files from under MC and have it apply its internal database tags to the WAV files). You control what is imported by specifying the file types for import under the Folders, Edit > Audio section of Tools > Import... > Configure Auto-Import. Remove all folders that are not relevant to your AAC files; Edit the folder options that remain for your AAC files, selecting only type Audio and checking file type AAC. Disabling the others will prevent MC from importing other file types.
Once that's done, you can work the steps from the instructions provided in the links.
After you've accomplished this, then you can focus on (2), and for that a single Library is quite sufficient (and almost always the better solution).