Haven't tried it under the seats but I will next time. From past boating experience, you don't want anything pushing on the isinglass for very long or you will get a milky haze at the point of pressure.

It doesn't fit inside the trunk well, diagonally at best. In the mfg. pictures, they show it attached on top of a folded soft top - a bit bulky looking for me.

 

i leave my softop on my tj folded down for months at a time.

just make sure it isn't pinched or rubbing on anything sharp and you should be fine.

when i finially decide to put it back on (i know why) it is usually a little bit of a fight to get it stretched back out and kinda looks funny with creases all over. however, an hour in the sun and it looks like new.