Anyhoo, Linux is all about choice. As this is a tutorial, I thought it would be helpful to jot down the steps. Here is the path I found works best.
1. Install app. There are several options, but this is adequate for a single user looking for the current version:
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sudo add-apt-repository ppa:mkusb/ppa sudo apt-get update sudo apt-get install mkusb usb-pack-efi
3. Cleanup. The reason I only use 95% of the remaining space for the persistent partition is that I want to leave room for wear leveling. Quit mkUSB, open GParted and delete the usbdata partition on the USB drive (space becomes unallocated). Also, sudodus doesn't mention anything about not mounting the persistent partition, but I follow Laurent85's advice and disable automount for an mkUSB persistent drive (for "how to" in Mate, see here).
That should work for most folks. For more information, see official website (same link as Spearmint2 gave above), especially the discussion of persistence, the Quick Start Manual, and an omnibus thread on the Ubuntu Forum. See also Linux Uprising, DebugPoint and How-To Geek.
BTW, a large persistent drive has useful applications, but I still think the better solution for most situations is full install to USB hard drive.