I picked up a can of Bondo a while ago; I haven't gotten up the gumption to try using it to fix some holes in my car's body.  Can anyone recommended youtube tutorials on this?  I heard panel replacement has become standard now by professionals.  Too expensive IMO.

If the holes were cause by rust then you really need to do the whole panel or cut it back to good metal and weld in a new piece. 

 

If you don't get rid of all the rust you are just hiding the problem.

And you have to seal the inside also, no matter which method, or it will rust through again, in a short time.

I cut out the rust with my Dremel tool, then pop rivet in a piece of galvanized duct metal (just did this today on my Impreza). I also spray undercoating on the back side of the patch panel. In the past, such repairs have lasted 5 years or more before rusting though again

Stevo F has the right idea.  You must cut out and inch beyond the perforation.  If the hole is 2 inches, cut a 4 inch hole, at least.  I use some naval jelly to convert any rust beyond the hole on the backside, rinse off the jelly & dry,  and then spray the backside with undercoating.  The hole can then be fiberglassed and bondo it.