The ferry to Tagbilaran (and Panglao) does not accommodate vehicles. You can likely rent a motorcycle there. I recommmend the Bohol Bee Farm resort for a stay on Panglao. Quiet, friendly place and the best food on the island. (People come by the busloads...literally....every night for their ribs. Get ther early.) I have never been to Apo Island, but if I understand correctly, there is not even a dock there...you wade ashore from the ferry....so no motorcycles.
Enjoy.
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