I'd run both engines off the same tank. I know many like to run off each tank seperatley, and this is good incase you have a load of bad fuel, that way you do not clog both engines, but if your boat is not sitting and you have extra filters onboard, that should never be a problem. You should be adding startron or a similar product anyways to condition the fuel to be safe anyways, especially if gas sits in the tanks for a month without usage.
The reason I would not ever run off each tank seperatley is this....it is hard to monitor both tanks, you have to toggle between them to see what the level is. Yes, you will try and keep them about even, but this is not that simple since it is rare to have them the same size and over time they will vary. the other reason is if you go out and have a 1/3 tank and go further then planned, you have no reserve and no back up. If you were running off one tank and always have the other filled with atleast 1/2 tank, you can switch as a reserve and run in safely.
I had an instance where my father used the boat and told me we had enough gas for a few more trips, got down and it was low...1/4. I wasn't going far, but was boating at night and would never have gone on that low fuel, but I switched over to the other tank with 2/3 fuel and was safely able to boat.
By drawing off each tank seperatly you will never change the trim of the boat, just allow it to rise and fall in the water colomn due to weight and the boat will always ride the same. It is typical that most boats due better on efficiency at certain fuel loads, so buring off one tank before another is ideal to get to that condition. Each boat varies and only trial and error can show this because each boat is loaded and run differently.
As for a design aspect, there is no reason the fuel cannot come from both tanks from a mechanical standpoint, but this was NOT the intent of the designer. I am a Naval Architect and design boats for a living. If the builder intended to have the boat run with a tank for each engine, they would have built 2 side by side identical tanks and run the tank off each respective side for each respective motor, that way they siphon fuel the same. This is proper design for a 2 tank system if run primarily for each engine.
By having 2 tanks, a Main and an Aux, the designers intent was for you to draw off the Main for typical use anfd the Aux when additional fuel is needed. As designed, the typical boat model would be better running more off the main tank then the aux, but you have to remember, you add options that might not be standard or typical to what the designer thought, or you add gear and people onboard, that changes, especially on smaller boats under 30ft. With that said, it is possible you may see better results with the aux as your primary tank actually, I know some guys with Marlin's actually claim this.
My recommendation, use one tank at a time. I run off my Main more then my Aux, maybe a 60-40 split. I start with 2 full tank for the year. I run my aux down to somewhere between 1/2-1/3, then switch to my Main tank. When that gets down to 1/2 or so I make sure I fuel up and top off my Aux, or both again. If I topped off my Aux only, I will run off that next and have the Main as reserve. If I top both off, my Aux gets burned off first since I run better with a lighter load in my Aux tank. I never let a tank sit for more then 2 weeks without being used.
Another option is to use your Main most of the time and use it like you normally would, top it off run it down to maybe 1/3 and refuel. And only put 1/2 fuel in the Aux, and every time you refuel, run it one trip and get it down to 1/3, then go to your Main tank again, run it normally and when you refuel put enough fuel in the Aux to get it back to 1/2 again. Run the Auc 1 trip and then go back to the Main for typical use. This keeps your boat lighter, hauling more fuel around then you need cuts down on efficiecny and wastes money, but you do not want fuel sitting and being unused for long periods of time. By using it that one trip each time you fuel it should never sit for too long, but also leaves you enough fuel for reserve.
If your talking about a smaller model like a gulfstream or seafarer with a big Main and smaller Aux, this is the best method. If your on a bigger boat with similar sized engines like my 265(130g-120g) you can run it either way.
As a Naval Architect, I size and locate fuel tanks as part of my job, we have stopped designing our tanks to be draw off of from each engine, only the Main tank can be drawn from for engine use, the other tanks are only Aux tanks and the fuel most be transfered to the Main tank for usage. Only our flagship model allows you to draw off 2 of it's 4 tanks simulataneously, but we tell customers we do not advise running off 2 tanks at once. The only reason you can draw off 2 tanks is because the boat is large and the fuel transfer system is easier to transfer to a mid tank rather then the Main aft tank which cut down cost and ease of the mechanicals onboard, the boat also runs best since the mid tank is located near the CG of the boat, giving it the best ride with fuel here, and it does not effect the trim much on the boat as it runs. Ona boat this big there is a significant gain as fuel burns, on our smaller boats we will not see a radical change like this boat experiences.
I would advise you to run the boat the way the designer intended to be run. They designed the boat with the mindset that this tank configuration will be run a certain way and will provide the best results for the typical user with a typical boat. Not all boats are rigged the same, so this can vary a little. I know Grady has little opinion on this, but they do very little of their own design, most of the work has been outsources to C Raymond Hunt. To Grady, they will allow whatever is mechanically feasable because they want their owner's to do what makes them happy...they feel it keeps you happy, which is true, but may not be the best advise from a techinical stand point. If it will not harm the mechanicallys, they see no problem with it, but they are giving their input from that point alone, they are not taking into account all the other variables that will change with how and where you siphon fuel for use.
