I am working with three departments - should I list them as separate co-applicants on the Application Form, or should I include them in our institution's costs?

It depends on the activities carried out by each institution in relation to the project work. If it is a research activity, they should be involved as co-contractors, but if it is a smaller scale activity, e.g. one-off data analysis, it can be handled by a service from the bidder's budget.