In a multi tank set-up, both of the main tanks can supply the header tank simultaneously.
In the example you have described, I would call the two tanks that are side by side the "Mains", and the single tank the "Header". Both of the mains can feed the header at the same time, and be emptied before using the fuel supply in the header tank. The header should then feed the UAT, which ultimately supplies the pump with fuel.
Connect the main tank pick-up lines to the vent of the header. I like a seperate line for each main tank to feed the header tank. I don't use a tee, except in the main tank vent system. That requires two vent connections at the header tank. Make each line the same length.

Remember one thing: All of the tanks are on the suction side of the fuel system. They should be connected together with large diameter tubing because the little bitty pump has to work real hard to draw fuel all the way from the "Start and Taxi Tank" then through each main tank, then through the header, then into UAT before it finally gets to the pump.

I prefer 6mm tubing, with all connections safety wired with .020 stainless safety wire. Any air leaks on the suction side will result in air bubbles bring introduced into the line. The line that goes to the pump inlet should never be allowed to leak, (suck air) as bubbles might (always will) end up going through the pump to the engine. Some pumps cannot process bubbles, so one big bubble will put the fire out, always at the wrong time, place and altitude. Install your filter (In the pressure line) in the vertical position, to keep from trapping an air bubble inside. Any air in a vertically mountyed filter will be pushed out during the engine start.

On the vent side, I use Tygon F-4040A (yellow colored line from Du-Bro) from the main vents (tee'd together) to the drain tube on the bottom of the fuselage. Bevel the drain tube toward the airstream in order to put a little inflight ram air pressure into the vent line. That will help the pump suck the fuel.

It's okay to have the tanks mounted at different levels, but onlt if made necessary by the design of the fuselage. The BVM MiG has a low mounted header tank, and it works just fine.

Any leaks on the pressure side of the system (downstream from the pump) will result in fuel under pressure spraying into the interior of the aircraft. I've already seen this happen. It can cause a spectacular in-flight fire! (and usually results in the loss of the entire airplane).

I hope this helps you.

Harley Condra
BVM REP
Team Jetcat.