re: CAD to CNC Machine Workflow

That is my problem as well for laser work. The software has the ability to create "project libraries" where notes and other details can be saved. My problem is I'm always in a rush to get to the end results and I never spend the extra minutes to detail the little things like setups, etc. that make the parts come out better.
Usually I'll open up a year old file and think "what the heck was this for?" 

At least it keeps things interesting!