overall code organization: helper, library, core, or model?

@sneakyimp

On the other things: Download PyroCMS (2.1.x or 2.2.x - I am not familiar with the newer ones) and Bonfire 0.7.x and review code for their solutions. I've learned from them mostly. Other ready yet systems might be helpful too - compare and choose features, adapt code, check third-party code for upgrades. Don't go making everything alone, hunt for ready features.