I just rooted my Marquee and ive read countless threads trying to figure it all out. but some things im still stuck on are
1. if you download a theme does it have to be made specifically for the rom youre running
I'm not big into theming so I don't know for sure, but I think themes are usually built for a specific rom. If you are having trouble finding a theme for your device/rom here is a universal guide to help you do some theming of your own: http://androidforums.com/faqs/633037-guide-how-wip-easy-theming.html
2. are there app markets designed for root users?
I don't think there are any big root markets around yet. Maybe because Google allows most of the root only apps in the play store...
Here is one to check out: Fireplace Market
and
3. can sprint detect that you are rooted
They can't tell without looking at the phone if that's what you mean? They might suspect if you are abusing free wireless tethering and they can cancel your contract if you are. They could certainly tell if you brought it in for repairs. They may not notice if you returned to a stock rom though. That said, Sprint doesn't really care about rooting. Here is a link to their official policy on dealing with rooted devices: Sprint Root Policy which basically says to inform the customer of the risks of rooting, and then follow normal procedure with replacement or repair.
dumb questions i know but i havent been able to find the answers