Perpetuum Minor Issue

Im missing something really simple. Perpetuum requires you to copy paste program into separate folders to open multiple accounts at once. Boxer is only looking to one folder, how do i get each section of screen to look at a different folder?

Thanks

[MiRai]

Normally, ISBoxer's virtualization takes care of things when a game client doesn't want to use a single folder (assuming everything is set up correctly), but you can look at this if you're using multiple game folders:

http://isboxer.com/wiki/Multiple_game_folders