İ think the starting self question of margin note is,
- you want to edit directly on nodes/captures (detailed one document work, maybe you like more pencil usage etc)
- you want to just summerize your nodes / or want to create new a note from referenced multiple document
if its one you should focus on mind map and get everyting on mind map
if second you should focus links and try to create as much as links from your captures/annotations.
İ mean just create annotations with organised colour or hashtags as you wish.
for first (1) question’s answer: you can check it out these links.
it will make usage easier for you and get most in short time
good luck 