You can rename the current folder with the help of MP3tag if you apply an action of the type "Format value" to _DIRECTORY.
In general the starting point is the current folder. The more information you supply for the renaming, the less relative becomes the target folder.
So, the safest way to end up exactly where you want to be, use a full path including drive letter to describe the target folder, e.g.
e:\music\%albumartist%\%year% - %album%
The other thing with two variables. And the more I think about it, I come to the conclusion that only one is good enough.
The whole thing is only necessary if you want to modify the filename of the flac file and still know which wav file served as source. If this is irrelevant, then you can leave out all of the next stuff.
Now, you say you have these files:
00. Artist - Title.flac
00. Artist - Title.wav
Only the flac file can store data in tags.
Create an action of the type "Format value" for OLDFILENAME (this is the name of the user-defined field. You will only see this in players that know how to cope with user-defined fields. And in MP3tag):
Format string: %_filename%
This stores the current filename in the field OLDFILENAME
You say that right now the wav-files have the same name except the extension. So everything is fine now.
As it may happen, you might get the idea to modify the filename e.g. because you spotted a spelling mistake.
You can now filter for files where the current (flac) filename does not match the contents of the field OLDFILENAME:
$if($eql(%_filename%,%OLDFILENAME%),1,0) IS 0
Files that appear in the list show that the current filename is not the one that has been used for the pair of flac and wav.
You can now use an export script to create a shell-batch-job rename the wav file so that it has the same name as the flac file again:
$loop(%_filename%)ren %OLDFILENAME%.wav %_FILENAME%.wav$loopend()
Execute that batch-job and the wav-files should be renamed.
Finally, because every thing is fine now, you can perform again the action that I described above to store the now vaild name for the flac-wav-file again.