Yup, thats correct. As
headcrab said, sticking to much power in can fry them. So make sure you buy an amp that matches the wattage of your speakers. Whoever sells you this should (you hope) be able to sort you out with a system.
As for your question about the cueing software would work fine, it would be no different with a surround sound system, you would just need to select the Aux Sends it goes to.
Nick