Perhaps the best way to create an innovative company is to hire a bunch of people from a number of diverse backgrounds, keep them comfortable, fund them unquestionably, allow them to market their creations, and give them complete freedom for their schedule.
As far as clerical work is concerned, keep it simple. If possible, eliminate it. If elimination is not possible, use computers with a programmed intelligence to manage work in such a way that it does not suffocate the workers.
The company should be optimized such a way that the workers have nearly unhindered time for creativity. After all, it is hard to focus creativity if you're trying to keep from falling.