It's really meant for use with RCA. It allows you to group fields together for reporting purposes. For example, I might want to group countries together into regions for reporting purposes, so I could make a Region field organizer that I define with country values. Then I can use this in model related reports in RCA. There's a limit of 3 active at once.
The field organizer can also help you with troubleshooting what fields are mapped where, and also allow you to group fields when pulling (non RCA) reports. If there's a group of fields that you want Marketo to look at as a group (say product usage?) you can group fields there as well.