I made sure to put all the original bolts back in place. Like others, I installed a tie-down loop using the original bolt on one side and I use it to secure my ghetto-blaster subwoofer.
For the gaps on the wheel hump, I used some rubber mat that matches the cargo mat and made little covers. The covers tuck under the panel and secure with the original bolt.
Instead of using rubber, EVA foam could be used. Maybe this weekend I'll make a couple covers as proof of concept. EVA foam can be painted to match your interior if black isn't your style.
^good idea on using that old rubber mat for the wheel well holes and securing with the bolt! I have several old all-weather mats from prior vehicles, as well as carpeted ones, so I'm definitely going to try something like that.
I do not have all the bolts re-inserted. I put them in a Ziploc bag, labeled them, and stored them indoors with my seats.