Generally, you are allowed to divide the site as you see fit, as long as it's clear you're not gerrymandering the site to suit specific credit requirements. In other words, there's no specific right way to do it.
You may want to look into creating a 'campus boundary' that includes the whole site and separate 'project boundaries' specific to each project. The three project boundaries do not necessarily have to add up to equal the campus boundary (e.g. the project may contain an on-site retention pond that falls within the campus but not any of the individual project boundaries). You can choose which credits refer to the campus boundary (likely stormwater quantity and quality, landscaping water use, light pollution reduction), and which credits refer to the project boundaries (materials credits, waste management, etc.).
From what I can tell from review comments from a similar situation, consistency in metrics is very important when more than one project is submitting documentation based on elements that are shared by multiple projects.