After the coolant has been drained (or leaked) out, to refill it correctly you must remove the little allen plug by the thermostat, and then fill until coolant comes out that hole. Then reinstall the plug. This will get "most" of the air out of the system. you'll probably still have to check it daily (cold) for a week or so, as it will probably require a little more each time until all the air is out of the system. It is best to get the proper pink Hybrid Organic Acid Technology coolant (HOAT) from the stealer and mix it 50-50 with DISTILLED water. Obviously, first make sure the entire system has been checked and there are no leaks, loose clamps, etc.
Right now you're probably having the heating problem because of either air in the system or a bad thermostat. If you change the thermostat, get it from the stealer (IIRC ~$30), as it is the only place I know of that you can get it with the stock o-ring seal. If you get an aftermarket thermostat, it doesn't come with this seal and you'll have to use a gasket. I've tried this several times, and it almost always leaks/seeps. I've tried numerous different gaskets and the only gasket I've found that works is the Fel-pro P/N 35840. Bottom line, it's just less hassle to bite the bullet and get the stock setup from the stealer.
As a side note, if you do replace the thermostat, make sure that the little bleed valve on the thermostat is at the top when you install the stat. You'll see it if you take it apart. If it's not installed on top, it'll be more difficult to properly bleed the system. Also, while you're at it have the radiator cap pressure checked. It shouldn't be bad, unless someone has previously messed with the system.
One last thing, if you're mechanically handy, do it yourself, as most "run of the mill" mechanics are clueless on working on these things......some Jeep dealer mechanics included. Many will just throw any old coolant and tap water into. Do this and you'll have big time problems down the road.
06 GCO, Dk Khaki, QDII, Flshing Hi 3rd Bk Lt, MDS "ON" Lt, Airtab Vortex Gens, Debadged, Fumoto Drain Valve, BT Catch Can, Chopped EGR Tube, SRT8 CAI, K&N Filter, Sonnax Trans Line Press Booster, SC Tuner W/Adv Trans Tune App, DS Tuner, Cust tubular hdrs w/3 in Magnaflow/Xlerator AP Exh Sys, Bilsteins, SRT Springs/Sways, Cust Eng Cvr, SRT8 frt/rear bumpers, FRI Sidewinder Cam/6.1 valvetrain, SLP 25% UD Pulley, BBK true 90mm T-Body, SOS Ign Coils w/.060 spark plug gaps, SRT Reps with 265/45&295/40X20's.