The cage I have in there now is the Or-Fab bolt in style. It actually goes to the dash and then there are flat steel pieces extending to the floor. They are actually bolted thru the floor where the drain plugs were. I'm going to start by building a bracket that will be welded to the frame and then to the bottom of the cage. Then I figured I could weld a few gussets into the corners of the after market cage for added strength. For the rear section I'm going to go completely custom fab and do a new cross piece at the rear of the original cage. I'm also going to tie it into the frame right behind the rear wheelwells. I watched an episode of Extreme Off-Road the other day where they did just that.
Or-Fab offers a complete weld in kit, but at the time I bought this I didn't have the welding connection I do now.
I think it would be perfectly alright to add weld on pieces to the bolt on stuff. It shouldn't weaken it right?
Here's some pictures of what I have right now.
http://www.orfab.com/images/TJSportCageA.jpg
http://www.orfab.com/images/SprtCagetop.jpg
http://www.orfab.com/images/SBR200.jpg
http://www.orfab.com/images/SpcageWdown.jpg