The main concern is to keep a pristine, unmodded install available incase anything breaks ever.
All MultiSH3 does is change the Filemanager.dll to point the career files for that current install to a different folder. Generally you want to do this before starting the current SH3 install so it always knows where the career files are and creates it normally.
First rollback SH3 Commander.
In your situation you might try just copying MultiSH3 into each of your installs (GW and WAC) then run it in each one, using perhaps GW1 for the GW install and WAC for the other install.
Than run each copy to create the base career files. Than log off, copy the proper captain's career into each proper folder and try a SH3 Commander launch from each game. You should be fine... just remember to back up any important files (the careers themselves is really all that's not replaceable with some work I think) and be ready to reinstall if things go south.
