First obvious thing is to make sure you aren't storing anything thicker than the support bars under or on top of your bunk end mattresses. We would strip the mattresses down to no more than a sheet. If we tried to leave a blanket on top it would interfere with the canopy coming down well.
When our HW popup would not close well, it was usually due to the tents not being folded in just 'right'. Make sure the corners are unzipped before you start to lower the canopy - it makes it much easier to get the tents flatter and limits the corners bunching up. If you have a slide out, make sure the tents for the slide are hanging on the OUTSIDE of the camper before sliding in the bunk ends. Then, after the bunk ends are in, tuck the slide tent in as flat as possible. This helps prevent any damage to the tents, and again, makes it easier to get the tent flat before bringing the canopy down.
We would lower the top about 2/3rds way down, then take some time to carefully fold the tents in to keep them as flat as possible and avoid any major 'bunching' that happens if you just let them randomly fold up as the top comes down.
Then we would lower more until we were about 4/5ths the way down and do another flatten/tuck all the way around, then lower the rest of the way.
One thing to be especially careful about is to make sure the tents are clear from the cutoff switch. In our HW this was in the driver's side front (hitch end) corner. Feel up into the top canopy, just in the corner and you'll find a small silver metal push-in type switch. When the canopy is fully lowered, and the tents are not obstructing it, that switch pushes down on the camper body and 'engages' and shuts off the power draining items like CO2 detector, etc in the camper. This saves your battery from draining when you have it parked.
If you don't have the area clear from tents and/or you aren't getting the roof down fully it won't engage this switch and your battery may be dead next time you are ready to go out.
It took us several trips before we got it down pat on getting the tents arranged and flattened so the top would come fully down without any extra effort.
2012 Flagstaff V-lite 30 WTBS
2011 Ford Expedition
4 kids and a hubby & never enough time to camp!
2011: 17 nights 2012: 26 nights 2013: 46 2014: 20 2015: 16