Flask is preferred when your application structure is simple and small. Flask can manage things that way. But when the project structure increases. It becomes a troublesome task for flask. But when your app structure is very large then dividing the app into smaller parts is the best idea and Django does it really well for you.

I use Pycharm for Python Development and WebStorm for JavaScript Based development and for all other programming like C/C++, I use Sublime Text 3.

I use Python Django for creating APIs.

To begin learning python you should use Learning Python by Mark Lutz , I had read it when I started learning python it gives you overall picture of python and later chapters digs deep into the concepts explained briefly before in the early chapters.