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I work on DoD projects with varying project reporting requirements. There are many methodologies and processes one can follow. I've experiences success with Capability Maturity Model Integration and Agile (others here have mentioned agile too). There's an ongoing "meeting of the minds" of merging CMMI with Agile in the defense space.

For estimation, learning a bit of earned value management system (EVMS) can be useful. There is COCOMO II for estimation, but I don't think you need to go there for small projects.

A book I've found useful is "Software Estimation: Demystifying the Black Art" by Steve McConnell. Its helped me.

The secret sauce is to find that knife's edge balance of infrastructure (accountability and management) versus flexible productivity.

Then there is always the Scotty Principle.