Hard top is optional but in some places the dealers don't stock without them, particularly on unlimited. If you don't want you might have to order.
Standard is soft top, with optional hard top ($$, but $ credit to remove soft top) or both ($$). As others have said, the hard top won't fit in back. Its three pieces are two removable "freedom" type panels in front (which give the front seats an open roof) and one piece that includes rear seat roof, cargo roof, and cargo windows. The freedom panels can fit in back but the rear roof and windows don't fold up or anything, so they must be stored in a garage or so somewhere big when not in use. (search threads on hoists for ideas on storage).
If you want the quiet and warmth of hard top in winter, with open top in summer with a way to cover up quick, go dual. If quieter/warmer is not a big deal, go soft only. If covering up fast is no big deal, or you seldom remove and/or don't mind a half hour removal / install, go hard only. Hard top removal cannot be done without help, without a hoist.
I went dual (ordered in CO, stockers are almost always hard tops here). I love my hard top, last jeep and two prior BMWs were soft tops only. For road trips in summer, soft tops are a must. But hard top was worthwhile in winter, because if my top is up for a few months, might as well have as much sound insulation as possible.
2012 Crush JKU Sahara: Ordered 8/30, "C" status until 10/10, "D" until 10/15, built 10/27, unloaded 11/02, and delivered on 11/05!
The 3 piece hard top is the 2 front pieces and the hard top itself. The hard top sits on the jeep . the hard top is the side windows, rear window, and the top from the rear seat back.. It's not like a car hard top with just the roof section.The ones up front will fit in the back.