Sorry, I do not mean to talk over your head. To do manual Input configuration and linking using the SHN Utility requires knowledge of the configuration information and how it relates to link records and linking in general.
Each EXIOxx Input has configuration information. The EZIOxx tab, Inputs Settings and Monitor tab, displays and sets each Input configuration.
The Input Group number is assigned through this tab. An Input has no default Group number from a factory reset condition. I suggest assigning Input 1 to Group 1, Input 2 to Group 2, and so on. The remainder of the Input configuration information can remain with default settings. Using the Set button to link an Input automatically sets in the Input Group number. The Input Group number is the Group number that must be using in the link records in the EZIOxx and the PLM for the specific Input.
WARNING: once you set an Input Group number it overrides and suppresses Broadcast messages for that particular Input. Doing so probably breaks Indigo as I think Indigo is dependent on the Broadcast messages for Input state changes.
The Configuration Register is displayed on the right side of the EZIOxx tab display. The Read button will read the current settings, the Write button writes changes made to the Configuration Register. I believe Indigo is dependent on the Broadcast Status Chg option being set. With this option set Inputs which are not linked (and do not have a Group number assigned) will generate a Broadcast message when an Input state change occurs.
A good way to under the relationship of configuration information and linking is to look at all the information after a factory reset. Then create a Set button link for an Input. Now look at the configuration information and the link database to see what information was established using the Set button. All the same information must be set manually when creating it through the SHN Utility.