Late response, but in case you are still looking I don't think I have enough experience just yet to talk about my workflow. For the moment, I'm mostly fine with just running my entire notebook. And yes, my program is "scattered" across cells in a notebook. And that's useful. The blocks are the small units I would want to debug, or to document with markdown above the block.
However, you might look to Jeremy Howard of fastai [1] fame for some direction. He apparently built the entire fastai library using notebooks and nbdev [2] which allows you to "add #export flags to the cells that define the functions you want to include in your python modules."
I have tried out nbdev in my free time, and it's pretty cool.
[1] https://www.fast.ai/
[2] https://github.com/fastai/nbdev
