I am a little confused by your post. I have a Seneca as well and I will be picking it up from the avionics shop next week with a full Dynon panel. Do you have a picture from your engine monitor to better explain what it is you're missing and what you currently have? Our engine monitor shows two tanks graphics of fuel and how much is in them. Are you wanting to know how much each engine has burned vs total burn?
The graphics show fuel level based on level senders in the tanks. I am wanting the fuel totalizer to show total fuel used per side. The Dynon recommended K value settings for my system were way off. I added 90 gallons of fuel after the totalizer said I burned 60. I am now blindly trying to adjust 4 each k values (supply and return for each engine) without knowing the separate total flows for each side. Without being able to know the total amount used of each engine it is a guess to get the K values correct.
Do you have a return line that requires another transducer per engine? My installer showed my the fuel flow calibration page and told me that only one pin was used on each EMS for the fuel transducer and the other one does nothing. I know I will immediately forget which is which so I will put the same value on each pin for each engine. What I did find on that page that would probably be useful for you is a line for last flight fuel used for each engine. This would allow you to make more accurate pul/gal per engine if your transducers. I know the fuel used totalizer on the EMS screen is from the last fill up vs last flight but you should be able to get some more accurate K values by looking at the fuel flow cal page.