This doesn’t sound like “the SuiteCRM way” of doing things. The subpanels always show all the relationships to a related module. The “select” pop-up is actually a “select a record to create a relationship”, it is not a filter on the subpanel list, which is what you’re talking about.
Here is an example of changing the query for the subpanel, I don’t know if you can achieve something more through a different approach: