Jared,
There are a few ways a custom prompt can have multiple entries, and I'm not sure which way you're trying to do.
Do you want to prompt for project name and supply two project names?
To do that you would create a custom prompt for Project > Name in your report. Then when you run the report you would choose "Equal" under the Name prompt. You could then enter a project name and you would see a list of names to choose from. After choosing one project name you could start typing in another, and you could choose another name from the list that appears. If you run your report now you would see both of the projects you named.
Does this help? If not please provide more details on what you're trying to prompt for and I'll be happy to try and help.
Thanks!