Ah. I see. Sort of.
Yeah - do a 'crontab -e' and you edit the file and schedule programs. Not familiar with folding@home (in the sense of never having used it) but it's strange it would have to be run from a particular directory. Some programs look for configs in particular places, but usually have a command line option to tell them to look in alternate locations. You can schedule scripts to be run, so I suppose you could write a one-liner about 'cd /to/dir && folding@home' or something. Makes sense why you'd want to start and stop it at particular times, though. I don't think a 'killall' would present a problem. A last thing to check is whether the program can sort of schedule itself. Be a nice feature to have if it doesn't.
-- Oops. I was answering before your edit. That answers my last question.
Cron can be tricky with some things but it's pretty simple generally. You just have fields where you set the times and the commands, with '*' standing for 'all slots'.
Like part of mine is
#MIN HOUR DAY MONTH DAYOFWEEK COMMAND
10 15 * * * /home/j/sbin/slackchange
So at 3:10PM every day, it runs that script.
The only thing to do is export VISUAL=your-favorite-editor and run 'crontab -e', like I say.