I've only done the Sand Island - MH section, though we're (finally!) doing the lower section about a week after your launch.
We camped at the Mule Ear site, which is river left, and gives you easy access to Mule Ear and Chinle Wash, two great hikes on the upper section. If you have time, I'd say get the Navajo Permit. If you're blowing through the upper section, then probably not.
You can never step into the same river; for new waters are always flowing on to you. - Heraclitus of Ephesus