I had the same problem & found a quick/simple solution. Before RegEdit or even a long copy paste operation you might consider this:

1. Upgrade all accounts via the wow web site & your CD keys.

2. Install the expansion as normal to your first/main wow directory.

3. Hit start on your second copy of wow. You will get a Pop Up, explaining that you don't have wrath installed (for that copy of course).

4. Run the installer.

For whatever reason,The installer will update the one you just tried to start with no additional input needed. At least that worked for me, for 3 wow directiries on one machine.