Hi just noticed that when on the highway top flip flaps around near the rear window should there be something holding it down where the rear window meets the top, I found some velcro there from previous owner, but only on one side, near end of rear window where you can fit your hand between top and window.

 

Those staraps are actually from the factory - the glue dries out and the flaps start, well, flapping, making noise at speed. Some glue will solve it, or have the dealer take care of it if you're under warranty and want to bother.

 

could you just put some more of your own velcro on it. If so, would anyone be able to tell me where it was. I think mine off now to..

 

so there should be two velcro pieces on each side, also what straps, the white ones underneath the top, that meet the rear window.

 

No, its really just fuzzy felt, and it doesn't attach to anything, it just protects the top from the sharp edges of the plastic trim that is under the glass.

 

I wouldn't expect my top to flap around if it was located under my hood.