Whenever you penetrate the hull
, you should use a sealant of some kind. If you want the attachment to be there permanently (forever and can never remove it) use 3M 5200. If you want to be able to remove it to replace it then use a polysulfide sealant (Boat Life) makes one. If you just want to make a gasket
then you can use silicone sealant. All are messy to use so mask any area that you don't want the sealant to dribble. I would try very hard to make a backing block to match the curve of your inner hull and the same with the outside when you are ready to attach your motor
lasts forever, Oak is good if it is painted, Doug Fir if you don't mind replacing it in a couple of years.
You have the option of touring several boat yards there in the SF Bay
area. I like the one out in Alameda that has lots of boats to look at and compare. I can't remember the name of it. Maybe Olson?
Screws are only a good idea if you cannot reach the inner hull to use through bolts. If you do a pilot hole and then force a screw in your fiberglass
it will break the glass and weaken it surround the screw.
Good luck in your projects.