I did something similar on my previous JLUR and will be doing the same on my 392.
Run with the hardtop from November to sometime in March. I use a Sunrider Flip Top during these months for any warm spells. Ditched the freedom panels long ago.
Once the softop goes on, I run with it down 95% of the time…maybe more! For me, it’s main purpose is to be able to close when a pop up thunderstorm rolls in. The rear windows live in my garage, except in rare situations such as road trip. With the doors on, windows up, and softop closed, I’m protected from the elements. Heater and AC work great in the JL! The safari style top keeps the rear relatively dry in most situations without the windows. My 392 is a third vehicle, so it doesn’t get left outside all day at work and spends it’s nights in a garage. YMMV
I also have an Alien Sunshade (mesh), but usually hold off for the first month or two in Spring. But when it starts getting hot, (Charlotte) I’ll throw that on to cut down on the direct sun.
If you really aren’t sure, I’d recommend starting off with the hard top and adding the Sunrider Flip Top immediately. Kind of the best of both worlds. If you find you want more, you can buy the exact same softop from Bestop or MOPAR, after the fact, easily.
Congrats and looking forward to seeing pictures!