Run the same pressure as the fuel system. I will run the 2000+ Corvette fuel filter that has the built in regulator at 58 lbs that way it's consistant with my system. The trucks seem to run low on pressure at idle but boosts the pressure up under performance mode. With the stand-alone system you can do anything to your truck you want without worrying about running out of fuel for the juice.
With a fuel pressure safety switch installed in the stand-alone system all you have to worry about it too much bottle pressure or running low on nitrous. Too much, lean, too little, rich. I'd suggest getting an electronic bottle gage if you can afford one. My bottle is in the bed of the truck and I don't have time to get out and check the pressure. On a hot day I've seen 1300 lbs of pressure on the gage! I think you're only supposed to spray between 900-1050 PSI. Tune it for 1050 and let it be fat on gas should it run a little lower. BTW, Dynotunenitrous.com has a bottle heater with a FPSS for about $100.