I place everything in the stowed/collapsed/zipped position except for leaving the door zippers and the clear vinyl window zippers partially open to allow air to escape. As for the center hoop, I have found the tent to set up much more cleanly if you extend the two outer hoops first, and then the center hoop last to "pitch" the roof tight.
I've got the same tow rig and it's a pleasure to tow the Roo with.Cool setup. I have a 2004 Weekender Transcontinental that I tow with a 2004 V8 4Runner. I've been leaving everything wide open when I fold up and just tucking doors and other canvas in as it closes. I'll have to try some of the tips in this thread.