Command Interface Reference v1.0 (2013) by Gideon Zweijtzer - Although the title suggests this is only for the Ultimate II, this document is also valid for the Ultimate II+ and Ultimate 64.  Here is the overview as quoted from the document:

The ‘Ultimate-II command interface’feature is a new feature for the 1541 Ultimate-II module. It implements a way to communicate to the 1541 Ultimate-II programmatically from the Commodore 64, through the cartridge port I/O registers.

The‘Ultimate-II command interface’is the communication layer between the C64 on one side and functional modules of the 1541 Ultimate-II on the other side. Such a functional module takes a command, and returns data and status back to the user program on the C64.

This document was obtained from the 1541 Ultimate official Github repository and should not be considered the most current version.  Please visit the Github project for updates and other related documentation.