Piecing Together Python, Command Line, and SQL

I’ve never posted anything on any board, and full disclosure I’m almost done with the CL lessons so my questions may be premature or flat out dumb. Apologies if either but would like to know if the former. Here goes…

I need to understand how everything ties together. How do I set up files? When does a person bang away on the command line, when do they open a GUI, how does the command line, Django/Anaconda/whatever come into play when developing something? When writing Python code, what should I use? Ultimately one can run calculations and document their project in Jupyter but I want to learn alongside developing my own ideas. I have a bunch of algorithmic formulas I want to apply to data, do I write each one as its own function and save in different files or do I put them in a Python file names formulas? I get the command line code and I get the Python code, but what do I do?

Again, this is probably rudimentary stuff. Im not an idiot (depending on who you ask) and have a degree in ChE so I’m very technical in thinking. I’m OBVIOUSLY not a developer or programmer but I’m WAY into it. I’ve built simple stuff in VBA, C++, FORTRAN, and have a decent understanding of SQL, HTML, Ruby on Rails, CSS, and whatever. I just want a big picture view of seeing a problem (which you “know” the solution but need to build the program) organizing the steps to solve it by building a computational, data-heavy, formulaic, user friendly I/O.

I don’t even know what to Google which is why I’m posting. Thanks for any of your time.