I personally leave mine in and just work around it, not that big a deal for me. I got racks for cargo.

 

your dealer & Chrysler can and probably will deny any claims involving the top (hard or soft) if you keep the soft top on when you have the hard top on since they specifically say to remove the soft top when the hard top is on. i personally don't care what you do, but wanted to mention that.

 

The vibration of the soft top rubbing against the hard top tends to wear holes in the fabric. I believe that is the concern.

I would take it out. It only takes a minute to through it back on. I cant for the life of me figure why you would want both in there. Even if it's because of lack of storage, just throw it under your bed.