First let me address your seal concerns. Auto-Rx will have no negative impact on the seals. Magnatec is run in all kinds of vehicles every day without any reported seal incidents being any more common than similar synthetics.
You really have no choice other than deriving some cleaning benefits of Auto-Rx that is already in the engine sump. This is not a very good oil for running Auto-Rx with due to Auto-Rx being polar and a good part of the Magnatec being polar. The ideal environment for Auto-Rx to clean is for Auto-rx be the only polar ingredients in the oiling system. With the magatec in the sump the polar ingredients of the oil will be competing for the same metal surfaces that need to be cleaned. The end result is that the Auto-Rx will work at a slower pace. I would suggest running you current sump fill with the Auto-Rx for only 5000 KM. It will be important to run GTX during the rinse phase of the application. You do not want a polar oil when you are trying to rinse contaminants off the metal parts.
If your motor has fairly sizeable amounts of sludging, you will need to run a second application. You may also wish to change out the oil filter at the half way point of the current oil change, if the motor is very dirty.
I hope this answers your questions. If not please reply.