He's talking about the XM radio antenna. I would think a good place would be either right on top of your sound bar, or that empty spot between the sun visors right under the footman loop.
You can put 5.25" speakers in the dash with an adapter and 6.5 will fit in the sound bar, using the grill cover it came with. I would never put 2 12" subs in a jeep. You would blow your ear drums! One 12" or a 10" in the rear will be just fine, also less to steal if they get it off. There are tons of DIY and factory made sub boxes that you can look up to mount behind the rear seat. Most will bolt to the tub and are covered when the tailgate are closed. So it is pretty safe from thieves and removable. If you make it tall enough to block the handle for the tumbling rear seat you will have a small lockable trunk too!
Nalin 5.25 dash speaker adapters.
, Probably the nicest one you can buy. Do a search, there are threads with dimensions for making your own.