I don't know if you'll get answers that really enlighten you.. At least for me, how I go about a project varies based on what I'm doing.
Some of it starts out with a solid idea of what I want, and then tackling parts of it, then putting those pieces together and applying whatever "glue" (metaphorically) it requires to be a completed project. Very rarely could I ever draft a procedure from start to finish until I'm done. Even then, I would probably do some things differently. If I did it again, I'd probably change further things still. Revisions, ya know?
I find the stress of trying to get everything right the first time is not usually worth it. So, I pick a place (code, the enclosure, a breadboard with the key components, whatever..) and get the ball rolling, then build around that. Maybe I'll make the PCB next. Or find where it'll live permanently (if it will be permanent at all), and imagine what parts will be on a front panel, accessible after it's built, and then design the PCB. It all depends.
My most complex completed project so far is a powered subwoofer. I had an unusual 6" subwoofer I found and bought years ago because it looked interesting, but I had no plans for it. So, one day I decided I was ready to put it to use. I found plans for a horn-loaded enclosure made for that speaker. It looked relatively easy to build, had incredibly low response (down below 40Hz), and it's esoteric (which I like), so I got the wood and made the box.
Then, I needed an amp. I knew I'd first need a power supply, and those are generally simple, so I started there. I got a toroidal transformer, some high-power diodes, large caps, and pos/neg linear regulators for the preamp stuff. You can hardly go wrong, but I simulated a basic design in software, and it seemed sound, so I ordered PCBs. Turns out, I didn't get the right pinout for the negative regulator, so that went up in smoke. Easy fix, but another $90 in PCBs and a week for delivery. Tough teacher, but I won't make that mistake twice!
I had been looking at some of the National power op-amp ICs, which seemed easy to use, so I found some schematics, and designed the amp PCB. (Couldn't really test it due to the pins not being particularly breadboard friendly.) The first PCB worked OK, but had some grounding issues, so I revised it. Second one worked great.
Obviously low cost was not my prime motivator. By now I could've bought something nice for the price in parts and PCBs. But what fun is that?
I wanted some fancy features -- a variable crossover, gain control, auto power-off -- so I found examples online and built what I could on breadboards. Each stage is basically a block you can build and test by itself, so I did just that. The auto power-off part was the hardest. I found something similar, simulated it in software, tweaked some values, then decided I didn't like the flaky response, so I redesigned parts of it, simulated again, tested with real parts, and finally got what I wanted. Then, I designed the most densely populated PCB I had ever made up to that point. I printed it, tested the fit of all the parts, checked each connection, and then checked them again. I went over all the ground points, all the positive and negative power pins, the signal path.. and ordered those boards too. Success on the first time! Still found something I'd like to change, but it was a minor tweak.
Finally, I found an ad for a site that will design metal faceplates in the back of Make magazine. I carefully measured all the controls and mounting holes, reading data sheets and verifying with a ruler. Then, I printed my design and put my PCBs and parts in / on / through it. After a few fixes, I sent the design off for manufacture and got back the powder-coated plate. It was almost perfect -- had to enlarge one hole a little with a Dremel.
The last step is to cut a hole in the box, have a metal backing enclosure made for the amp (so it doesn't leak air through the holes in the plate!) and paint the box, but I've been enjoying it so much that I haven't wanted to take it apart long enough to finish it.
So there ya go. I don't know if this is exactly what you're going for. Did you have something in particular you're stuck on?