What you want to do is run your Rotella synthetic oil for 3000 miles on its own as the rinse phase for your completion of the Auto-Rx application. Then dump this oil fill and rebatch running the maintenance dose of 3 to 4 fluid ounces of Auto-Rx with each oil change. This level of Auto-Rx should keep your rings from binding from contaminant load, or coking. This will ensure that your ring packs are free from binding and keep a good seal with the cylinder walls. Minimizing unburned veggie fuel from proper ring wall interaction should be very helpful with your green fuel efforts. I highly recommend not to run Seafoam or other solvent additives in the crankcase/oiling system. With that said, you may choose to run a solvent or Seafoam as part of the fuel side of the equation, in attempt to keep the intake system clean.
Tell me more about your two tank system. Are you reacting spent cooking oil to remove glycerine before filtering for fuel in your diesel? Are you attempting to run this fuel at 100% or as a supplement to petroleum diesel fuel?
Perhaps we have two fish to fry in your questions. From the oil sump side of the equation it is not a good idea to introduce anything to the oiling sump that will detract from the oil film formation on cylinder walls. Auto-Rx is your only lubricant addition that will keep rings clean of deposits without sacrificing lubricity. As well as keeping piston rings from coking up and becoming ineffective, Auto-Rx is also helpful in maintaining oil film strength on the cylinder walls, which is also part of the seal, keeping blow by gases from entering the oiling system to start with.
In conclusion, run Auto-Rx in the oiling system. If you feel the need run some solvent in the intake side have at it. Your goal should be to keep solvents and unburned fuel gasses out of the oiling system. Tell us more about your two tank system of recovering spent veggie oil.