Hi Tammy,
I think of the organziation of Workfront like this... The Portfolio is the file cabinet sitting in the corner of the office. The Program is the drawer on that filing cabinet, the Project is the folder in the drawer, and Tasks/Documents/Issues are the papers in the folder.
For our agencies that use project intake forms, we usually setup a request queue (so a project you turn into "Publish as a Help Request Queue). There is a custom form attached with a series of questions and then we attach routing rules so it is assigned to a team (the main person and their back up) that "processes it". They work with agnecy executives to see if this project is doable and who will be the PM for it. Once that decision is made, the processor converts that issue into a project, puts it in the correct Portfolio and Program and then changes the Project Owner to the PM who will work on it. The PM then creates the project plan from there and off they go!
Also, look at Queue Topics too as you can show different custom forms and have different routing rules depending on how automated you want the process (i.e. Digital projects got Bob while Print Projects go to Jill)