There's several ways and approaches to repairing holes/dings/knocks in aluminum and sheet metal in general. The pics in your build aren't good enough/close enough to see what might be the best approach. Can you post close ups of the damaged area, both in and outside of the boat?
Some approaches:
1. Rework the damaged area with auto body tools till it's close, then either weld the tears or place some extra aluminum sheet over the tears and weld it on.
2. Completely cut out/remove the damaged areas and weld new metal in place of the damaged metal.
3. Reshape the damaged area, place new sheet metal on one side and weld on the other.
4. Same as three, except place new sheet metal on both sides.
5. Rework the damaged area, then reweld, but don't use any new sheet metal.
6. Don't do anything but a nasty weld to close over the holes, which you already have. Looks ugly, but is functional.
Post up some close up pics and I'm sure folks here can suggest a "best" and better approach for you, depending on your budget. BTW, budget is going to affect your choices in these areas along with how long you plan to keep the boat.