To get started, you can choose between using the Arduino IDE to write your code in, or use a Makefile build system. What you choose should be personal preference, and it's very simple to switch between them for a project should you change your mind later.

Arduino IDE	Standalone with Makefile
Only a single .ino file per sketch	Need to keep sketch code along with a Makefile
Set options (HSE value, board variant, libraries) through IDE	Set options in Makefile
Recompiles every time (bug?)	Faster to recompile
Uses stm32flash to upload	Uses stm32loader.py to upload
	Not recommended on Windows

Choose:

Makefile Setup, or
Arduino IDE Setup (recommended on Windows)