Yes, you can run the stock sub with your new HU, and yes, you don't need to get the external amp, but why not? It will sound so much better. I have the 6800 and it's a great little HU. My set up is simple. I have a 4 way amp running the components up front, and a mono amp running my 2 10's.
Don't feel taken .... feel thankful that you are going to have a nice little system!

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Black Cherry, Rock Rails, Roof Rack, VIP Alarm, Tint, 3M Protection Film, Tow Hitch & Converter,
Pioneer P6800DVD,
JL 450/4 Amp,
JL 500/1,
JL Prowedge,
Fosgate 3Sixty.2,
Morel Elate 9 speakers,
Momo Shift Knob,
Nitto Terra Grapplers, TRD Exhaust, QuickShifter, CAI, Shocks/Struts.