By keeping all change orders in writing, you can keep track of mounting expenses. Don't be afraid to spend your reserve, but don't spend it all the first week of construction. Finally, the best way to manage your job site is to be kind to your work crew, and when deserved provide treats, nice bottles of wine or beer, cash bonuses, and compliments. You may want a third-party to mediate. Know when payments are due and how much they'll be.
Some contractors charge weekly, some monthly.
The payment schedule should be agreed to in writing before the job starts. Know how problems that occur after the job is completed will be handled and who pays. Make sure your contract gives you a way out if problems are insurmountable. An attorney who specializes in construction contracts can help you with the necessary language.