Enlist a Neutral Party
Don't try to run a draft all by yourself. Always try to recruit someone who's not going to be participating in the league to help out.
One of this person's duties will be to keep time, so that you can focus on tracking the progress of the draft, recording trades and taking care of your other duties as commissioner.
The neutral party can also be given the final say in settling disputes that might affect owners' results. The person can maintain the draft board and keep track of the order in which owners will make their picks on each round. The goal is not only to take the weight off your shoulders, but to remove the appearance of bias. Remember that you're not only the commissioner but one of the owners, with a vested interest in the draft outcome.