The traditional way of billing this sort of project would be:
1. A shoot fee, often based on a day rate and your best estimate of the time involved, plus any expenses incurred, and sometimes post-processing at about half your hourly rate for shooting. This includes providing proofs of the images to the client, for them to make their selections.
2. Licensing fees for the images they select to use, based upon the exact details of the usage.
There are a number of factors to consider in each case. In addition to what's been recommended... I don't know if its been updated lately, but the book "Pricing Photography" gives good guidelines for licensing fees, language for written agreements, generic forms you can adapt for your purposes, etc.
There are some other pricing models being used today... Just be careful not to give away your work too cheaply. A lot of people seriously underestimate what they should charge for commercial work. For example, your day rate should be calculated using a cost-of-doing business analysis, with reasonable profits added on top.