I have this system in place, two 23L plastic tanks, one each side feeding to a filter via a fuel switch valve and onward to an engine.
I keep mine there as a reserve fuel system. During long hauls, I don't use them.
Some food for thought, Dan: Will you use the deck tanks first or last? If first, you will be watching them as they run low and have to switch 'em early in case you airlock, leaving about 4-5 liters in each one.... If you use them last, same problem but you've already sucked the main tank dry
If you use jerry cans, you can top up the main when possible and not worry about switching. There's very little faffing with jerry cans if you use a couple of jiggle siphons to fill them into the main tank/s (i.e. no spillage). Top tip - if using jiggle siphons, run the lift side through a length of light plastic pipe - keeps the suction point low in the can