IMO the problem with bondo is it can crack the slate when you try to disassemble. I think bondo is a mistake to use. I've seen tables where people, in an effort to clean off bondo, sand the slate leaving waves in it. That makes for some interesting rolls. Not to mention beeswax is neater, faster and easier to apply and has all the give qualities you need.
edit ...
as far as application, I like to stick a rod into a chunk and as I use the torch to melt the wax, I simply move along the seam about 6 inches above the table surface. After its in, you can further flow it out with the torch, put on plenty of extra and wide as you need. Let it harden and skim it off with a sharp putty knife. Remember to allow extra time for the center screw holes if your table has them since the wax is deeper there and takes longer to dry.
I've also learned not to use wedges to level the slates since by their very nature they work their way loose and create a problem. Thin flats of wood are the best way to go.