When boxing a frame I always weld "bolt couplings" where mounting holes were for every item that was bolted to the rails and or frame just in case I ever needed to unbolt something I would never need a hold back.

If your frame is already boxed as you mentioned, enlarge the holes to accept the hex couplings which are roughly an 1-1/2 inch long. Insert a bolt in the coupling and weld the coupling slightly below the the top of the rail. The hex design makes a good area in the hole for weld peneration. TIG and or MIG is best for this task. Take your time doing this and constantly turn the bolt so it will not swell in the coupling. Because the coupling is so much longer than a nut chances are that the threads will never stip. I also use an anti seizing compound on the bolt when welding so the heat will not cause it to swell or seize. If you have the time and equiptment you can make your own coupling to any desired lenth from round stock further assuring stripping the threads, but I think an inch of thread is more then enough. Remember, once these are installed you have no room for adjustment so be sure of where you want to place them.

You could always cut a hole in the side of the already boxed frame to thread a nut the original way but chances are it will require the help of someone else to give you a hold back on the nut underneath the vehicle. If you do this be sure to file the edges of the hole to save yourself or your friend from cutting up your fingers and hands when installing the bolt.