At the moment I have 2 command line folding windows open for my dual core CPU to work on.

I would like to have them disapear and run in the background.

But I would also like to run and close them as I please. I do not want them installed as a service and running all the time. So is it possible to make them hidden?

Assuming your CPu is 64-bit, recommend you run the SMP client.

I run a service, but could manually start
cd foldingathome
./folding start
close the window

and finish
cd foldingathome
./folding stop
close the window