Firstly - nail down the geometry you want 100% before you get the process started. This will save you a bunch of time later, as if you have to tweak it later it often has minor effects elsewhere on the drawing (sometimes easy to miss unrelated things).
Don't be deterred if the first drawing you receive is off by a country mile. Not sure why this happens, but it seems to be common. Just send them a list of all the bits that need adjusting and the second drawing is normally pretty close. If you want to adjust the placement of welded-in hardware like bottle mount bosses or cable ports after that, the easiest method I found was to just amend the drawing by hand (I used red pen so it was more visible), scan the drawing and send it back to them.
In terms of tube selection, I gave them my weight and just let them choose for the first frame I had built - and it was very good. It is very compliant, but surprisingly still puts the power down well when you crank up the Watts. The first frame was a more conventional design, with a high top tube. The second frame I had in my head I wanted a stiffer frame, so I upped the tube wall thickness (with a more angular tube profile) on the down tube, spec'd a larger diameter top-tube and changed the frame design to one where the seat stays and top tube intersect pretty much inline with each other at the seat tube (like the Paradox). This combo was a mistake. It's no worse than a stiff alloy frame, but no better either (Does look pretty though!). I'm thinking (hoping) it will work well with a true-to-size 2.6" tyre out back setup single-speed, but I wouldn't want it to be my "daily driver" as it doesn't smooth the trail chatter like the first frame does (and does ridiculously well).
With my first frame I choose press-in headset cups, but they tend to squeak a little in warm weather. Having a Fox fork I assumed it was a creaky CSU at first, but I ended up putting the same fork in the second frame where I'd spec'd integrated bearing cups and it was blissfully silent, so maybe that's something to consider. I had been a bit wary of putting integrated cups on the first frame I ordered as I didn't know what the casting/machining quality would be like, but after seeing the overall quality of the first frame I took the chance on the second one and was pleased with the results. The casting and machining of the headtube is excellent and I would almost certainly go with the integrated cups again next time (I would only go press-in if I really wanted the option to run angle headsets easily, but if you're happy with your geo you shouldn't really need to...).