you need to get some pics up of your new baby!!!
congrats on the new truck! why'd you downsize?
They do make tonneau covers made for trucks with tool boxes and they are great! There are 3 different types that I know of. Here is the link to the site where I got mine. from the looks of your tool box the handles are high enough you shouldn't have a problem and now that I beat my problem I love it!
The other ones are less expensive but I went with the ExtangRT because I liked the low profile and didn't want the snaps