Do as you suggest above. Run a line to the transom and split to the two filters/water separators. Ensure the line is big enough diameter to supply enough fuel to both engines at WOT. Consider putting shut off valves in case you need to isolate an engine for any reason.
The order of parts should run - Tank - filter/separator - primer bulb - engine. Think about how you connect to the filter and engine etc in case you want to run either engine on an auxiliary tank for any reason. This can be done in many different ways to either connect straight to the engine or through the individual filters by using standard fuel line connectors in the desired places rather than hard connecting everything.
Freelance skipper, RYA Powerboat Trainer and Advanced Examiner