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.