I assume you've got a reversible pump on these bags? because there's not enough head pressure with aerator pumps to effectively daisy chain bags (or so I've been told). That said, a few ball valves would solve that.
I have a reversible pump that goes to two bags that are under the cabin and bow seats on the surf side. I put in a Tee before each bag, and then got a plastic ball valve so I could open or shut each one separately. There have been times where I would only want to fill one or the other, and having that shutoff makes it so I can for sure get them both drained well.
The ball valves, tee's, and barb fittings are super cheap at your local plumbing store.
I chose to have vent lines for each of them to a thru-hull. I could have used another Tee, but since I wanted to operate my bags separately, I would have needed check valves and a thru hull is certainly cheaper than adding more check valves.