how big is too big to use filler?

Weld em up......slowly! Those look thin and if you keep burning through, it will be all hell to get em finished up.

I'd use a hole saw or something that can cut that into a more manageable square or circle, then make a filler for that.  This way you ensure you're getting a solid piece.  If that metal is really thinned out (what you're trying to weld to), you'll have a difficult time even on the lowest setting to weld that decently.  If you wanted to not weld them, you could use a fiberglass filler like Marglass or bondo hair, which is waterproof, then go back over it with normal filler.  But, I would weld a plate in just to be sure.

tig it with a bronze rod.