yes. they are called chests. they go down under the rails and the tonneau cover would go over it. the only problem i would see with this is if you get a tri-fold, the 3rd fold might be over the box, thus making it a pain in the ass to use. i would suggest maybe a roll up one so all you would have to do is mount the box a little bit away from the back to allow the top to open. this is a picture of the box you would want..
you might actually be able to buy that exact box, check out the classified section and see if the guy parting out the 2008 ranger wants to sell it.
also i don't know if it's possible for rangers but i've seen it on a f150, but you might be able to get a over the rails box, and have a 4 foot cover up to the box.
and you should be able to find a tool box and or the cover online. and most of the time, the box will have free shipping.