I fly an amphibian with fibreglass hull over an Al tube frame.
Firstly you don't tell us exactly how the plane is constructed so it is difficult to know what to tell you, but in general terms:
Even in my plane the "non structural" fibre glass hull has structural application, a) stiffness, b) Keeping the water out, c) keeping the passengers in. It is not safe to believe that areas are non structural if you do not thoroughly understand the design and construction.
Repairing cored fibreglass requires specific technique. The areas to be repaired needs to be cut out and repaired in particular way for proper integrity. Again it is not specially difficult but it needs to be right. You can do it easily but if you have not done it before then you should visit a local specailist and let them tell you how.
The keel area needs to be structurally sound and watertight, rebuild it before you add another keel guard.
Micro baloons are used in boatbuilding for fairing (making smooth) rather than bondo, It is too heavy and does not act as an efficient seal. If you are proficient with other media, wood, metal etc, you should enjoy fibre glass however if you have not used it before i find out how first, either get a book and make a couple of practice pieces or go and ask a local fabricator if you can hang around and watch them do it, even help out a day or two.
Obviously working on a plane is a little different to working on a car or boat because weight is so important. You can't just build stuff up with loads of material, so again, it has to be done right.
Finally, if you have not flown off water it is absolutely vital you get training. It is not the same as land flying, much scarier and a good deal riskier to the uninitiated.