I agree with others here
that you do not want to use Bondo, or any other epoxy or vinyl putty, to fill in patches on the bottom of your boat where bottom paint has flaked off. When bottom paint flakes off a hull, it is a good idea to find out why and address that issue. I've found that when bottom paints flakes, it is mostly caused by too many layers of old paint and so it's time to chemically or mechanically get rid of those old layers of paint which do not make a good surface for new paint to adhere to. On rarer occasions, flaking could be caused by moisture in your hull, also creating a surface that new paint will not adhere to. You can usually delay the inevitable -- stripping the bottom -- only so long before you make this job harder than it has to be. You would be better served by sanding and fairing spots where paint has flaked off and filling them in with nothing more than more bottom paint -- until you bite the bullet and stip the bottom and start over again on a properly prepared surface.