I keep hearing that for large apps, using packages is key. I’m not sure what that structure looks like, exactly. Are there any good examples I could look at?
Yeah, check this one out: https://github.com/matb33/meteor-gift-ideas
It helped me get a sense of what an all-package app would look like. As the author mentioned, you might want to create an app-index package for your central layout
Maybe a little overkill! I was thinking something that has a lot of the code in a typical structure (client, server, lib, client/templates, etc) but a lot of custom and reusable functionality exists in packages.
Check out my socialize org on atmosphere https://atmospherejs.com/socialize and my demo repo for the messaging package https://github.com/copleykj/socialize-messaging-demo
Its a small example but should give a decent idea.