An easier way to play from 2 folders is just to go to your World of Warcraft folder, right click on it, choose copy, then choose paste, it will make something like "Copy of World of Warcraft" - rename that once its done copying to Wow2, then go into the Wow2 directory, right click on the Wow.exe file (RIGHT click), and drag it to your desktop, then choose "Create shortcut here" and then rename the new shortcut to Wow2.

Now, you can click your original WoW link for the first account, and click the Wow2 link for the second one.

Personally I run 5 at the same time and I have all 5 accounts in separate folders...the main account actually has 2 folders - one that is in full screen mode with full mods for when I'm playing a single character, and then 1 Wow1 folder with minimal mods and windowed mode for when I 5 box.