The softopper does have provisions for window storage, above the front seats. The OP is talking about completely removing the top, but taking it with in case of inclement weather.
A very nice feature of the softopper is that it can go from completely off to completely on in about 5-6 minutes. However, if you want to take it with you, that brings up some interesting issues. Now you have to figure out where to put the top and windows so they won't get damaged or be easy prey for thieves or vandals.
It might be possible to rig up a PVC tube to permanently fasten to the roll bar and store the top there, or behind the front seats maybe?