Quick overview.
The JTAPI subsystem is used by the IPCCX engine in order to control JTAPI access in to IPCCX. Hence, the JTAPI Role User you create should be associated with all CTI Route Points and CTI Ports. Looks like you have this correct.
The RM subsystem needs to manage and monitor Agent lines. Hence, the RM subsystem needs to be associated with all devices that are going to be used for ICD (ie, phones used by Desktop Agents, and phones used by IP Phone Agents). I think you have the right idea here, except for the fact these are CTI ports in your explanation (see below).
The users themselves need to be associated to the device they are going to use, and the "ICD Extension" radio box needs to have the line they are going to be using as their ICD extension checked. We typically create separate lines for this purpose to separate "personal calls" from "queue calls". I think you have the right idea here, except for the fact these are CTI ports in your explanation (see below).
Now, on the the CTI Port issue: The Agent lines themselves, unless you are doing something tricky you are not revealing to us in your original post, you do not want CTI Ports for the Agents' ICD extensions. Your options are to use another line on their hardphone, or to create a SP30+ if you plan to use CAD's Media Termination. Unless you're planning on using Softphone, I am confused why you would be trying to put Agents on CTI Ports.
So in summary:
1. Straighten out 1001 & 1002 -- move these over to hard phones, or otherwise sort them out as indicated above
2. 9999, 9001 should be associated to JTAPI (done)
3. Associate the agents to the devices containing 1001, 1002 respectively, and make those their ICD extensions (have to re-do this after reworking 1001 and 1002)
4. Associate whatever devices 1001 and 1002 are on to the rm user (will have to re-do this as well)
Good luck.
