While you build the prototype, you can refine your development techniques. You can hold code reviews and design meetings, practice using the source code control system and bug tracker, and set up the project's code directories. You can define the project's standard general coding style, naming conventions, indentation rules, commenting formats, and so on.
After finishing the prototype, the developers should get together and decide on any changes they want to make before starting the main development effort. These things are a lot easier to change at this point than in the middle of development.