When I booked my trip, I organized an itinerary with a tour operator. Once the itinerary was finalized, I wired payment for the tour and the Druk Air tickets to the Citibank account of the Kingdom of Bhutan.

Visas were waiting for me upon arrival in Paro. Visas are kind of an afterthought since you have to buy your ticket from the government who will only issue the ticket once you're cleared for a visa.

One more note about Druk. I flew Bangkok Airlines, BKK-REP in June aboard a borrowed Druk plane. It was was nicer than the Bangkok Airlines flight back to BKK. Also, you can often book DEL-KTM on the Druk flight that continues on to Paro. This avoids IC and can save money.