posted 02-04-2014 01:50 PM ET (US)
Don't overthink it. Just fill the holes with something waterproof. Just about any caulk would be fine, even the dreaded 3M 5200.I'd use something with less adhesion like 3M 4200 or 3M 101, but household silicone caulk will work too.
You can also fill it with expanding polyurethane foam which is very easy to ream out later, but the holes will appear brown. With a caulk you can choose white.
Be aware that some caulks shrink back more than others.
Whatever you use, mask the holes off first before applying your sealant.
I sometimes use clear shipping tape as a "mold" to get a flat surface on fillers that are very viscous. Apply the sealant to the whole and lay a piece of clear tape over it so the surface of it is flat and flush.
There are specialty caulks, polyurathanes especially, that are designed for very broad gaps and can be tooled more easily with a putty knife but I don't think running one these down is worth it.