It appears you have programmed the frequencies in channels 1 thru 5 in the bank, and that you have done it correctly if you are receiving talk groups numbers and activity. BTW, the system doesn't have to be in the first bank of your scanner so that the frequencies go in channels 1 thru 5. It can be in any bank, but the frequencies must go in the 1st thru 5th channels in that bank.
The talk group IDs (0-01-XXX) do not necessarily run in the sequence you listed in your post as an example for channels 3 thru 5. For the frequency in channel 3, for example, the 0 and the 03 would be correct, but the last three numbers could be anything.
If you are only hearing activity on the first two frequencies, it could be possible that they aren't using the other three or that there is just limited activity on them. A fire company in my area uses an LTR system with just two frequencies and they only work off of one of them. Never any activity on the second one.
Page 48 in the manual (Step 3 - Programming ID Scan Lists Manually)
tells you how to program a talk group ID, which in this case would be 0-01-xxx). Page 49 under "To enter a LTR ID" explains how to specifically program the LTR Talk Group. The Area Code is the first number (0), the Home Repeater is the second two numbers (01), and the ID is the last three numbers (xxx).
Page 28 explains how to program text tags. You can label a Talk Group or frequency by selecting the letters and numbers you want. When the TG or frequency (for a conventional system) appears on the screen, your text tag will appear also, enabling you to know exactly who you are listening to without having to remember the frequency or Talk Group.
For example, when my LTR system becomes active, the TG 0-01-108 appears on the screen and under it my text tag reads "Jackson Twp. FD FG 1"
You can also put your scanner on ID search by pressing and holding the trunk button until ID SEARCH appears on the screen, then release it. It will then search for and you will hear all active talk groups in the system. When one that you don't have programmed in appears, just push Enter and it will automically go into the next open spot on the ID Scan List. If you push and hold the Search button again until ID SCAN appears on the screen, you will only hear the Talk Groups you have programmed into you ID Scan Lists.
I may have given you informatiojn you are already aware of, if so, my apoligies. If I have helped, great !! If you have any more questions, just post and I or someone will help you.