1. Folders
since this will be your primary system, then the recommendation by others to use Documents by Readdle will work. If you'll be transferring files between your iPad and other devices/cloud storage then Documents will simply get in the way.
2. Mouse support
As mentioned before, no native mouse support within iOS. If you use your iPad Pro to remotely access other systems then using Jump Desktop (remote desktop app) on the iPP allows you to use the Citrix X1 mouse with it. That mouse will work on an iPad Pro but within Jump Desktop only. Works great!
3. Notetaking Apps
My recommendation is a combination of Notes.app (built-in note app) and OneNote. Both are great on the 12.9 Pro.
4. Pencil use
Currently the Pencil can be used both as a stylus for navigation and note/draw/writing.
5. External drives
I highly recommend one of the
RavPower FileHub devices. I have the one that I linked to and it essentially acts as a personal portable cloud storage device.