MacBandit:
That would be great. Currently, to use both processors, you need to use the command line version and the terminal. I have some scripts and I'm working on documenting the process for those who are Terminal-phobic. If you consider yourself to be okay with the Terminal, I can help you get started quickly.
Falleron:
Tiaguinho and I have been talking about doing something toward a folding control application. We cannot know how long this will take to achieve. I will be working on the back end and he will be working on the GUI part.
Still, if you want to run the other processor to complete one, it's easy enough to change a shell script to stop prior to downloading another work unit. Yes, it's not a beautiful way to do it, but it's efficient.