Ed,
How large a hole are you talking about. If you are thinking of the ones on the backs of the sponons on scale hydroplanes i suspect they were used in the real boat to service the fuel tanks.
Also, if you are going to race the Eagle in the IMPBA you will need to remove the sponson backs. We can not have notched transoms in the IMPBA.
I have an eagle all the wood work is done. Its a very nice boat and there is not a thing wrong with the wood in the kit. Im not sure if its going to be my race boat for 2007 but I think the old PT super sport raced its last summer.
Also, I do not seal the insides of my sport boats unless i have an opening in the structure. But if you are, your best doing this with a finishing epoxy.
Enjoy
Grimracer