Im not sure about the storage of the jack... but I can tell you a little on the bed cover. I am not going to get into brands but I will give you the main 3 types....
Solid Bed Cover:
A solid bed cover will cover over the rails and sit ontop like it is part of vehicle, and looks nice because it painted like the vehicle. The downfall to these are they have a hing that allows it to open from the rear (like a hood) but its limited range and hard to reach stuff in the from of the bed without getting in and crawling, and it can sometimes be heavy and hard to remove if you need to put something in your bed taller than the cover.
Vinyl Tonneau Covers:
A vinyl cover is decent as well, these lays down over your bed to cover the stuff inside it. You would have to get a good one that rolls up at the front of the bed because some dont roll up and have no side rails and will allow water to run down into your bed. The bad part with these are they can sometimes be torn easily and the "winch" can jam or runin the cover.
Folding Truck bed Cover:
The third more or less the best of both worlds. Its a hard plastic fold cover, it sits down like the vinly cover but its hard plastic and folds up in three sections. The nice thing is the whole thing is not fully interconnected and you can access stuff in the front easier.
I hope this helps, good luck.