Your pump decision will somewhat determine your thru hull setup. Aerators will generally empty out through the side while reversible pumps will push the water back through the pickup. Either way you need side thru hulls for venting. There's nothing wrong with using a single thru hull for multiple pumps as long as it's sized appropriately. You could get away with a couple of 1100 GPM pumps on a single 3/4" intake but a 1" would be better.
Aerators would probably be better in your case because you could buy two now with the appropriate fittings, some wire, and a length of hose to do your "manual" fill/drain for this season. Then, next season buy 2 more of the same ones and set them up for your automatic system.
If you go ahead and plumb your vents out the side this season it will make it easier to multitask while filling them. Connect the pump, throw it overboard, do the same on the other side then handle other business around the boat and just listen for water to start coming out of your vents and go unplug your pump and plug your bags at your earliest convenience (They could overflow overboard like that all day).
If you don't do the vents now it will require a little bit more attention because you will have to manually "burp" the bags and be more attentive to how full they are. The expense would be minimal to do the vents now ($5 hose, $5 for a plastic thru hull, $10 for fly high/flow rite fittings, and another $15 if you want a check valve on there) for the convenience I think it would offer.
Want to take it one step closer to auto? Do the above vents then buy 4 aerator pumps instead of just two ($30-40 each). Screw one pump directly into one of the bottom fittings of one of the bags (The Rule 1100 GPMs are 3/4" and screw directly into the Fly High threaded holes with no adapters) and connect your 6-7' length of hose to it. On the other end of the hose connect another aerator pump and secure the wire up the hose nice and pretty with some zip ties. Wire up each pump to one side of a 2 position rocker switch (The one on the bag to empty, the one on the end of the hose to fill). Repeat this setup on the other V drive bag.
When you're ready to fill throw the pump on the end of the hose in the water and flip the switch to "fill". The pump will pump right through the "empty" pump on the other end of the hose and into the bag. When it's full pull the hose back in the boat and position that fill pump above the top of the bag and the water will not come out. You could mount a hook or something to put the pump on so that it stays above the bag (Alternatively you could get a 3/4" cap to put on the pump's intake when done filling and just let it sit anywhere).
When you're ready to empty throw that "fill" pump back overboard and flip the switch the other way. The empty pump will pump right through that fill pump.
At that point next season all you'd need is about another $100 worth of stuff (Bronze thru hull, bronze valve, a few more feet of hose, etc.) and some time/tools to make it fully automatic.