Those would be the control channels for trunked radio systems and should be programmed as part of trunked system. They should not be entered as conventional channels since they only carry data streams as you have already heard.
Rather than simply trying to read, understand and retain the entire manual; I would suggest that you goal yourself to learn specific tasks one at a time. For example:
(1) What is the difference between a trunked radio system and a conventional radio system?
(2) How to program a conventional frequency
(3) How to program a trunked radio system and its' frequencies. What is a Site?
(4) What is a talkgroup ID and how do I add them to a trunked system that I have programmed?
(5) What type of trunked systems are being used in my area? Edacs? Motorola Type I? Motorola Type II? LTR?, etc.
The list of tasks to learn is endless but those above are a start. I would have the scanner in front of you as you read thru the Easier to Read Manual and actually try each task as you are studying the manual. The real benefit to doing so is to begin to get a feel for the logic (or lack thereof) of how various menu items, tasks and functions are accessed and/or executed.
Programming by computer and software is much faster and easier to master BUT ultimately, you will need to know how to operate and control the radio manually.
Not knowing what State, County and City you reside it makes it diificult to advise further. You may be able to find someone near you in the States forums that can give you very detailed information for your local listening area or other help in gettin you ap and running.