This is how I would break it down:
1. What do I want to make?
2. What topology do I want to use?
3. What's the detailed design?
for example:
1. What do I want to make?
A dirt pedal with a weird ass filter hooked to it. Filter before or after the dirt? I don't know, that could be an experiment.
2. What topology do I want to use?
A twin-tee filter and a bazz-fuss (because they are simple, cheap, and low part count)
3. What's the detailed design?
I don't know. I'll do some reading on how the part values impact each of those circuits and fiddle with it (Earthquaker style, because I don't know how to simulate it, what to look for, or what I'm doing in general)
or:
1. A Rat! With an HM-2 style tone stack (like those drunk beaver things)
or:
1. A parallel distortion with a blend knob
or:
1. Hook a green ringer to something (and then add a simple boost, paint it with a Patrine Cross and sell it for $800. . . badda-bing!)
or:
etc, etc