can it be run nohup - so that it can run even when I don;t have an ssh session?
Use screen:
screen -S miner
"miner" can be anything, it's just a name that you can use later to get back to it. This will give you a new shell. Start cgminer there.
Ctrl-A, then Ctrl-D will exit the new shell and will keep cgminer running.
To verify that it's indeed running in the background use this:
ps auxwww | grep cgminer
You can now disconnect SSH etc. To get back to your cgminer:
screen -D -r miner
Or conversely you could just edit the miner_start.sh script in /opt/minerpeon/startup/ folder and replace the existing cgminer string with your path and custom commands.
With the updated info saved your config will be retained and automatically loaded everytime the RPI starts up (which can be handy if you experience a power loss or the RPI crashes/reboots on its own).