I think the process starts with an idea of what kind of style you want. Then you draw up loose sketches. Then you draw the thing out 1/2 size on a large piece of board/paper/living room wall. You need to know the exact dimensions and layout of the engine, its mounts, wheels, forks etc. You then to ask yourself about the oil tank, battery location, style of gas tank, what kind of seat - will it need springs, where will you mount them, footpegs location, will you be able to reach the handlebars comfortably, etc etc etc.
Then you need to make the jig that will hold the rear axle and engine (so the sprockets will align perfectly) and the headstock at the required angle (bearing in mind rake and trail) in a perfect line; level in 2 dimensions and plumb. Then you need to buy the right kind of tubing, then you need to borrow, make or buy a bender - not a pipe bender - a tube bender; big difference. Then you need to bend the tube at the correct angles and notch it (make a circular 'mouth' at one end) so it mates perfectly. Then you need to weld it, bearing in mind that every weld will cause the tubing to move around - losing alignment.
Now, I'm sure many will say this is all nonsense, that you could do it over a weekend. Yes, you can. But you'll end up with a badly handling, dangerous p.o.s that you'll eventually take $300 for on ebay just to get the wretched thing out of your life.
