Basically having the fat cap up is so it will baste itself. Having it down will work out fine but you can always flip it if you want.
I like to bring mine to about 180 then pull off, cool completely and reheat the next day by steaming.
Some people will foil while doing pastrami but I have found it works out perfectly fine just pulled off and cooled.
When are you planning on eating it?
Like everyone else said fat cap is a peferrence of the smoker. Foil some do some don't. I don't until I'm done smoking it then foil and in the cooler for resting. after about an hour start slicing or if you need save it for later. It's all up to you andd your doing just fine.