ALPA Merger Policy lays out a process and several guidelines, but doesn't have a methodology for integration. In practice, Jim is correct about relative seniority playing a large factor in most arbitrator decisions, but it's not codified in ALPA Merger Policy.
Merger Policy follows a simple formula:
1. Direct negotiations between the two pilot merger committees to try to reach a deal
2. If that fails, go to mediation to see if a mediator can assist in reaching a consensual deal
3. If that still doesn't work, go to arbitration, and arbitrators are directed to take into account various factors such as career expectations.
For a JetBlue/Virgin merger, expect largely straight ratio within status (captain and FO) with maybe some extra slotting near the top for JetBlue pilots to account for a pilot group with a longer average length of service, but not much.