For a new custom from the maker, you can contact most makers directly. Many of them are here on bladeforums.com. There is an incompletel list of links on my site. Most have websites and e-mail these days and, of course, you can call. I should really update that. A few makers ask that you go through their dealers.
I usually prefer to meet my maker personally at a show. I find that we can have a good, interactive discussion, maybe go out for drinks. It's a good experience.
Price? Everything from free to at much as, in my case, $8500. The average for a simple custom balisong is gonna be about $350. Most makers will want some deposit. Some will insist on payment in full before work begins. In several cases, I've simply asked a maker to make me a knife, they've done so with no discussion of price, and then when presented with the knife I've had to ask, "How much?" Then, the maker will shyly say, "Oh, it's not very good. Maybe $X." My response is, "It's wonderful and I won't give you a penny less than $Y!" (Y > X). The maker then responds, "Oh, it's not worth $Y. I could never take that. How about $Z?" (Y > Z > X). And I say, "Ok, it's a deal!" So, we end up negotiating in reverse.
A couple of important things to remember: first, this process takes time. I've waited years for custom balisongs. Don't try and rush the maker. It'll only make things worse. Second, don't come to a maker with a blueprint and say, "Here, build this." These men (and women) are artists. It's ok to bring a few ideas, a few requests, but let them have some creative space to express themselves. You'll get a much, much better product, something that's true art.
? BTW.., Chuck already graciously offered to do that,-without me begging-, just to clarify.