Open the root directory for the first copy of the game. Create a text file (using Notepad or some such thing) called paths.dat. In that file, type
on the first line. On the second line, type
("Name" can be whatever you want.) Log into your first copy of the game and get to the character selection screen. Log out.
Now go to the SECOND copy of the game, and repeat the process. This time, type
Log into the second copy all the way to character selection.
You have now created custom folders for your characters. You can use the instructions located here to move your old settings into these new folders.