Replacing rusty body panels

Sorry to post this in the detailing forum but I don't see another appropriate forum to ask this......(body work forum?). Anyway, I just swapped a guy my 89' wrangler for a 94' bronco. The bronco needs some panels replaced due to rust and I've gotten a good start. I've cut out and welded in a replacement for the right rear quarter panel. I've ground the welds down some and I think it's almost ready for filler. My question is: Is Bondo the next step? If so, do you follow the Bondo up with a thinner filler to fill in the shallow spots or just use straight Bondo all the way? Also, someone told me not to grind the welds flush because the metal will get too thin around the welds, does this sound correct? The metal did not warp too much ( I went really slow ) but there are some low spots that need to be filled in.

 

Thanks for the info.! That's kind of what I thought I should do.