You can run 2 subs off one amp. Yeah, the best way to do it is to get a deck with RCA outputs. The deck doesn't have to have subwoofer RCA's if the amp your using has a crossover in it, but radio's with sub RCA's usually have a sub level control built into it so you can turn just the sub volume up and down through the head unit, which is very nice to be able to do.
And when you buy the RCA's, don't get dirt cheap ones like from Radio Shack. They allow noise to get into the signal easily, sometimes they cause turn on pop, and they can even put out lower sub volume vs. a quality set of RCA's. A good set of RCA's will cost around $40 for a 16ft to 20ft cable, it's worth the investment, they'll keep out the noise and send a strong signal to your amp.