The way SETI suggests doing this is to make an entry in your crontab.
That way if SETI stops running for some reason (usually a communication error back to berkely) it will automatically restart without rebooting.
Here are my crontab entries:
0 * * * * cd /home/cfarley/seti; setiathome -nice 1 > /dev/null 2> /dev/null
15 * * * * cd /home/cfarley/seti; setiathome -nice 1 > /dev/null 2> /dev/null
30 * * * * cd /home/cfarley/seti; setiathome -nice 1 > /dev/null 2> /dev/null
45 * * * * cd /home/cfarley/seti; setiathome -nice 1 > /dev/null 2> /dev/null
cron will attempt to start seti every 15 minutes. If it is already running it ingores it. If it fails to start, it will try again 15 minutes later.
The SETI Unix README:
setiathome.ssl.berkeley.edu/README.unix.txt
There is a nice PHP script I found to display your SETI stats. There is a link to it on my homepage. I'll send it to you if you're interested.