Ok, so I have been thinking about how to integrate Auxiliary Systems into the Campaign System we have developed, and this is what I have come up with so far. The last item is an attempt to make it more difficult for players to have a bunch of 0 CR auxiliaries consequence free.
Comments anyone?

Science: Guiding ships into uncharted space is not as simple as pointing at a star and telling the Helmsman to “take me there.” While space is undeniably vast, it is also full of dangers to any starships which traverse its expanses. To find their way through previously unexplored regions of space Empires equip their ships with specialized scientific equipment to locate, analyze, explain, and in short, find the safe way to get from one place to another. Campaign Effects: To move from a star system hex to an adjacent hex that has not been previously occupied by any unit from the controlling Empire a Task force must have at least 1000 SUs of Science equipment. This total is cumulative for the entire Task Force. If a Task Force does not have at least Science(1000), it may still move to an unexplored hex, but there is a risk that ships may be lost in transit. For each vessel which moves to the unexplored hex, roll 1D6. On a roll of 5 or 6 that ship is considered destroyed (or lost in hyperspace, whatever you like) and removed from the game.

Cargo: One of the most difficult things for any Empire to do is to keep its front-line forces supplied. It is not always practical or even possible for a Task Force to travel to an Outpost or Starbase for re-supply, and because of this an Empire may send Cargo along with a Task Force to help sustain it. Campaign Effects: During the Re-supply Phase a Task Force that is not in a system with a friendly Outpost or Starbase may use the Cargo carried along with it to re-supply its ships. First, total all of the Cargo(#) carried on all of the ships of the Task Force. The Empire may then supply up to that number in Combat Rating Points on any or all of the Task Force's ships. If the total number of Combat Rating Points exceeds the available Cargo, the Empire must choose which of its ships to supply. Ships cannot be partially supplied to lower the number of cargo they use, or to bring the total right up to the Cargo available without exceeding it. For example, Task Force 1 has a total available Cargo of 556. The Task Force is made up of three ships with Combat Ratings of 124, 345, and 466. The controlling empire may choose to re-supply the vessels with the ratings of 124 and 345 (468 total points) or the ship with the rating of 466, but no other combination is legal. Cargo expended to re-supply a Task Force is considered “used up” and should be noted on the ship display of the ship(s) which carried it. Cargo may only be replenished in a system containing a Friendly Outpost or Starbase.  All of the expendable munitions (including Probes) and small craft on those ships which are re-supplied are replaced in full. Marines and Ground Troops are not replaced.

Repair: Warships are always in harm's way, but an Empire may not be able to pull them back to a Friendly system to repair battle damage. To help keep their ships in the best possible fighting condition while keeping them “at the front” Empires make use of special Repair Equipment. Campaign Effects: During the Repair Phase a Task Force that is not in a system with a friendly Outpost or Starbase may use the Repair equipment carried by its ships to fix some of the damage they have taken. For each Repair(50) available to a Task Force a single point of Engine or Shield damage, or a single weapon system may be repaired (if using Critical Damage rules, 1 piece of Special Equipment may be repaired). Hull damage may not be repaired by these means, and can only be done at an Outpost or Starbase.

Hospital: While space battles are undeniably deadly affairs for the participants, a planetary assault can be an outright bloodbath. To help handle the casualties and prevent even more troops from dying due to insufficient care many Empires have vessels with specialized Hospital equipment on board. Campaign Effects: Following the conclusion of a Planetary Assault scenario (successful or not) an Empire totals up the number of Marines and Ground Troops which were destroyed in the fighting. For each Hospital(100) in the task Force from which the Assault was launched, reduce the number of marines or Ground Troops lost by 1. The controlling Empire then decides which of the Task Force's ships that the Marines or Ground Troops are placed on.

Transport: While the Transport Auxiliary system is most often used to bring in Ground Troops for an assault mission, it may also be used to replenish losses to other vessels. Campaign Effects: If Marines have been lost by a ship or ships within a Task Force, they may be replaced from troops being transported. In addition, casualties on board starships caused by “Crew-Killer” weapons may also be made up for by replacements being transported. Campaign Effects: During the Replenishment Phase a Task Force that is not in a system with a friendly Outpost or Starbase may transfer personnel being transported to ships to replace lost Marines or Crew. Each is replaced on a one-for-one basis. Each number removed from Transport should be reduced from the total Transport capacity, and can only be replenished by a trip to a friendly Outpost or Starbase, or a transfer from another vessel with “unused” Transport.

Auxiliary Escort: Often an Empire may choose to send a ship with limited combat capabilities along with a Task Force because of its Auxiliary Services capabilities. Obviously a Task Force Commander would not want to expose these vital ships to the dangers of combat, but they cannot be left defenseless either. Campaign Effects: When forces are chosen for a scenario a Commander can often choose to leave some ships out of the battle. If a ship (or ships) that is part of a Task Force is kept out of a battle and its total number of Auxiliary Services is greater than its combat rating it must be “Escorted” by another ship or ships. The escorting vessel(s) must have a Combat Rating of at least 75 for each vessel being escorted. This total can come from any number of vessels so long as it meets the criteria. For example, if three Auxiliary vessels are held out of a fight, the escort could consist of 3 ships each with a Combat rating of 75 or 1 vessel with a Combat Rating of 225. The consequence for not providing an escort could be great for an Empire. If Auxiliary vessels are left unescorted/under-escorted some or all of the ships could be lost (and not allowed to retreat). For each ship beyond the ability of the escorts or themselves to defend, roll 1D6 and on a result of a 5 or 6 1 ship is considered destroyed. The destroyed ship is chosen by the controlling Empire. For example, the 3 Auxiliary ships from above have only 3 escorts with a total of 150 Combat Points to protect them. With only enough “Escort Points” to protect two of the ships, 1D6 is rolled coming up a 5, resulting in the loss of one ship (chosen by the controlling player) to enemy forces (or SPACE PIRATES!) looking for easy pickings.