Hey Stephanie,
By ROI I'm referring to metrics that relate your program successes to your costs and the actual revenue generated. This is mainly done in RCA which stands for Revenue Cycle Analytics, Marketo's advanced reporting and analytics package. You may not have access to it in your subscription.
It's a big topic so I'd suggest you browse the community for articles on RCA or look for the "Beyond Basics" video course in your University link at the top and find the section on RCA/Analytics, which will go into it in a lot of detail.
I would have a unique program for every email send, so you can track success for each of those sends and reflect that up in your reporting.
The foldering is more of a personal preference. It doesn't impact reporting, so you just need to find something that's logical for you. The link to Josh's slideshare above provides a good example.