Good to hear!You're over thinking this. Stowing the windows is not a big deal, unless you're this guy:
I have only the premium soft top, no hard top. It's a fantastic design and a big improvement over the JK. I scored a MOPAR bag for free, but even at its unbelievably overinflated price it's a solid investment, IMO. When I'm not worried about getting caught in the rain to/from work (i.e. when my doors are off because the forecast is for high pressure) I don't even keep the windows with me. In the bag and in the garage they go...
I am anxiously awaiting the return of warm weather! You're going to love your soft top, I'm sure.
I'm thinking probably going with Mopar bag (tried to order with my JL but it was unavailable at the time for some reason). Most times I'll probably just leave windows at home - I have the luxury of living only about 5 minutes from work and could hightail it to my garage if a big storm came out of nowhere