Presuming its a mk 2 cover, I fit the sides, then position the apron roll under the opened boot lid. Then drop the boot lid enough to hold the roll in place. Then fix the centre stud and finally close the boot lid. Works for me.
Check that the popper is not damaged by trying it before anything else.
Also make sure the roof is folding down fully. I've seen roofs that sit high when dropped due to twisting of the frame, lack of lubed joints etc.