Right on the side of the battery tray the engine bay wall had rusted out a little but.. I plan on cutting it out and welding a piece of new metal into it. There is a hole that cut and had a plastic ring. the rust stops right before it and below the whole and to the left a little there looks like there was a indent(looking from the inside of the bay) The indent may be caused from the rust .. Is there a need for this indent or can i just weld a piece of metal there and don't bother with it.

 

Pictures would help to know what you are talking about but you might consider just replacing the entire apron. http://www.cjponyparts.com/product.asp?pn=BARK or http://www.cjponyparts.com/product.asp?pn=M116

Since it is cheap enough you could just cut out the part that you need and weld it in.