On page 19 of the MPR Supplemental Guidance (located here: http://www.usgbc.org/ShowFile.aspx?DocumentID=6473) guidelines are given for when small buildings located within the LEED project boundary can be excluded from the application.
Registering separate buildings as one project is not allowed. You can register them separately, and then use the 'block' function in LEED Online - this helps create a smooth application process for buildings on the same campus and/or under the same ownership/management. You can read about blocks in the help section of LEED Online.
Fees are based on the gross square footage of the certifying building.