Any headunit with an RCA out setup can run an aftermarket amp for subs. The headunit I run is a JVC run of the mill single din, I would look on crutchfield or bestbuy to check out the options out there. Anything which you use the wiring harness kit for your vehicle with, will utilize the factory amps and speakers, as well as having its own internal amp(aftermarket headunits usually have built in amplification).
SO checklist for headunit
$15 or so wiring harness-crimps to wires on headunit, allows the headunit to plug and play with the stock stereo system
Head unit features at least one RCA out setup to run to aftermarket amp
Dash Kit to cover any space not filled, and secure the radio
For sub setup
Amp, wiring kit for the wattage of the amp, running power wires down driver side of car RCA and Remote wires down passenger side.