The software development process has tackled many of the issues of file management, versioning, branches and information complexity. I have learnt the following lessons:
1. Use file revision control software for your schematics, PCB jobs, part libraries, documentation, test results etc. I use Subversion because it works, and the fact that it's free is a bonus.
2. Organise everything by part number. That way you can get from the MRP/ERP database to the directories and files.
3. Have a plan to deal with engineering BOM changes and stick to it. Some people edit BOMs and keep a list of changes that need to be incorporated when the PCB changes. Other people edit the schematic and regenerate the BOM from the schematic. Whatever you choose, make sure everybody sticks to the plan.

As for accounting hours to the correct project, I haven't found an answer except discipline.