How do I upgrade a WPMUDev plugin? Simply upload the plugin all over again?

Currently I’ve got past versions of 7 different WPMU plugins, and I think the reason for it was that the last time I completely erased my old Membership plugin and then put in the new version of Membership, but then of course lost all of my settings and had to start over again.

Am I doing it wrong? Am I supposed to just move the new file to the “upgrade” folder? Can someone point me to the directions for upgrading a WPMUDev plugin? There’s gotta be an easier way to do this.