I agree jhourcle, but just to make things more concrete:

1. The docs for your module's users go in your module's POD. I like xdg's suggestion of including a separate cookbook.pod as well. A tutorial.pod can be included too (since the main module's POD is sometimes more of a user's reference manual than a tutorial).
2. The docs for maintainers (or advanced users who might want to tinker) just go into the code as regular comments, since maintainers will already be looking at the code anyway.

And actually, there's a third kind of documentation that you might provide: A design doc. This can go in a separate design.pod file.

I think of it this way:

• As a new user, I'll read the tutorial to learn to use the module.
• As a novice, I'll use the cookbook and reference manual as-needed.
• As an advanced user, I'll dig into the module's code and will be grateful to read the comments therein.
• As any of the above I might want to read the design doc to get a better idea of how the module was put together (which objects/functions use which), why you made the design choices you did, how I might go about extending it (say, with a plug-in), etc.

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