The city of Bohol is mainly served by Tagbilaran Airport.
Flights to and from Tagbilaran to Manila take around 1 hour and 15 minutes. Domestic and budget carriers have daily flights.
It is possible to take a Roll On-Roll Off boat with your vehicle from Cebu to Tagbilaran.
Check out this blog for an indication of schedules – http://cebuboattrips.com/slow_ferries.htm
The Tagbilaran City Tourist Port serves boats plying the busy Cebu-Bohol sea traffic and major port cities in Mindanao.
A fastcraft ferry ride from Cebu takes about 2 hours.