I have found that the easiest way to keep my day job and startup separate is to have a separate laptop for both so that I'm not tempted to work on startup tasks on the company's computer while on the clock or off. Not too difficult to do during the day but it can be during the off hours when the company's laptop is better than your own.

I think the harder issue is trying to avoid answering emails that are startup related while on the clock. Even if it's webmail they still own the internet at work.