Regardless of the time of day you decide to fly, the ticket price will remain around the same. Book flights from Bohol to Koh Samui as you normally would.
Most people fly into Ko Samui (USM) if they book a flight to Koh Samui from Bohol. Ko Samui is conveniently located just 3.3 km from Koh Samui’s city center.
These are just IATA (International Air Transport Association) codes. They are used in aviation to identify and differentiate airports. That’s why a Panglao Bohol–Panglao Intl Airport to Ko Samui Airport flight would often be abbreviated as a TAG to USM flight.