unless hard drive space is at a premium, it's easier to just use a second folder.
If the servers use identical data, that's great. If they use completely different grfs, even better. If they overlap (i.e. they both use, let's say 'qdata.grf" and it's different for both servers, you're going to have fun renaming things), it can be iffy.
The only thing with multi-servers in the same folder is you'll tend to get a dominant one that will open all the time, even though you've clicked on another one. Separate folders are much nicer and easier.