Drupal nodes VS direct database I am writing my first Drupal module and am having a little bit of a hard time wrapping my head around when I should use nodes vs storing data directly in the database. Is there any documentation I can read on this subject or does anyone have any advice on this?

I've actually already written most of the module entirely using direct database access and my own tables. I am planning on open sourcing it but I want to make sure I'm following common Drupal development standards and I think this is the most glaring error I made. So now I am trying to figure out how much I need to move from my own tables into nodes.

What started me down this path of looking a nodes is that I need to implement permissions. The module has a bunch of projects and I need to be able to control which users have access to each individual project and all the data related to it. It's not obvious to me how to do that using nodes so I was considering doing this as yet another table in the database.
Typically Nodes are content. Permissions in a webapp are typically not content. Content is a piece of factual text, an image, an uploaded pdf.

It sounds like you want to look at the Organic Groups module.