I guess my projects flow kinda like this:
Idea →Sketch→Scale drawing (all the time thinking/changing/adding)—>Story pole. The story pole is vital for me in joinery to get my dimensions figured out. I usually wait until I’ve got all my ducks in a row (ha ha) and my materials ready.
The next step is stock selection, cut list, rough milling, stickering wood (and going back to first step as ideas hit me. Then final milling and hand plane all parts.
The building process is like everybody else: layout, joinery, dry fit,glue up.
As far as the condition of my shop, its a personal thing. I put all my valued tools away every night, I don’t worry about other stuff laying around.
I think one really important thing is work flow and having a dedicated assembly separate form your workbench is very important.