Does your car currently have the factory RKE? If so, there are leads that you can tie into with the aftermarket system which allow them to work together (so that the keypad on the door will still work, and disarm the new alarm, etc.), as well as the locks, trunk, etc.
It's actually easier to tie in an aftermarket system in a car with an existing RKE than without since all the leads are right under the driver's side kick panel. The most 'complicated' part at that point is just tieing in the starter interrupt.
If there's no existing RKE, it's a little more complicated, but not that much. Just takes a little longer tracing the leads you need to tie into.