I'm going to assume that there are three closely spaced holes and probably some older holes from previous transducers
Unfortunately,as others have said, yes you have to make the holes bigger and clean to fill them correctly....just epoxy from a 2 part syringe, or thickened epoxy(you have to buy way more filller than you will need), or polyester resin.
I'm going to assume it has bottom paint, in which case it doesn't have to be pretty so I would finish with a layer of glass over the area. (You will have to sand clean the whole area)
If you plan on adding a new transducer, consider wrapping a piece of plywood in glass and glassing it to the area. Now your new screws don't go into the transom...