I went there solo for 5 days in 2007, as part of a backpacking trip, and it's like this:
You contact a tour agent ("operator") and explain that you just want to see the sights for N days. (Many of their tourists hire porters for serious mountaineering.) You will be quoted the minimum rate of $200/day or whatever.
If the rate is different or the reply isn't prompt, try a different agent. His job is simple: hire the guide and driver, file the paperwork. In my case, the operator did not seem to own or "operate" anything, nor make concrete itinerary plans.
You wire the money to the agent up front. You're not in the country yet!
You should be placed in contact with the actual guide. Now is the time to finalize the itinerary.
Buy the obligatory one ticket on Druk Air or Bhutan Airlines. If you like Bhutan, you'll probably like the nearby parts of India, so it's sort of pointless to fly both ways, unless perhaps you have very specific plans.
Go there and enjoy the trip. The quoted rate covers all travel expenses, lodging, and food.
The only expense after the down payment is souvenirs, and anything you might do without the guide.
Unlike the rest of South Asia, there are no "tourist markets" for overpriced souvenirs. Actually, aside from one store in Thimpu, there was no souvenir shop at all. There was not one ATM in the country as of 2007.
Outside the (small) cities, the accommodations will be modest, because there are no hotels or proper restaurants. (There's still plenty of hospitality, of course.) So, there's no reason the rate would go up, unless you ask to spend the whole time in proper, urban hotels. But what tourist wants that?
I bought a small tapestry, some silver jewelry, and a few trinkets. The guide brought me to the market for the sake of getting any essentials I might need, not souvenirs. He was a little bemused about my excitement to buy random, ordinary things. (Bhutanese lawn darts!)
I bought a Gho before entering Bhutan, just across the Indian border. The guide said it was the better deal. At about US$70 (top of the line), that alone probably cost as much as everything else combined.
Once you're there, you'll see the reason for the policy. There are very few foreigners there, especially backpackers. The Bhutanese people are very curious and interested in other cultures, but they're also vulnerable and impressionable. The government is rightly cautious and even suspicious.
For the price of a fancy hotel, you get the run of the country and you'll never think about money once you're there. Once you cough up the flat rate, it's actually a backpacker's paradise.