Couple of quick things...Someone suggested eatiing a picnic on the Metro. Only if you want to get thrown off Metro. No food or drink allowed in the Metro trains or platforms, for the good reason that it attracts rats. National Archives is not your only Metro stop option; Federal Triangle is close to the museum. Check the "line" you're on carefully. They're color coded and easy to use.
Carts are plentiful near the museums BUT are strictly hot dogs etc. There is a cafeteria in the Natural History Museum with a variety of pretty good food and it's a nice facility but it is expensive -- all the museum restaurants here are quite pricey. As someone noted, Native American museum's restaurant is really expensive for a quick family lunch but Natural History's is more than you may want to pay--check it out. You might have time to go to the Old Post Office Pavilion (about a one minute walk, one block from museum) where they have a food court of different food vendors (Chinese, sandwiches, etc.) Not sure how pricey that has become.
As you go into Natural History, stop immediately at an information desk, get a map of the museum and decide what to see. Two hours is very limited and you want to see what the kids would like best. They may like the mammal hall and the dinosaur hall. There is a kids' hands-on room that most folks don't know about! The room's hours are kind of funky and limited so ask right away at the info desk if it's open when you're there. With such a short time in the museum you might want to skip it, though. Ask the info person if there are any special exhibits or hands-on events that particular morning. I would skip seeing an IMAX film if you only have two hours; it will eat most of your time there.
In Baltimore, the aquarium dolphin show is great last time we saw it. Aquarium can get VERY crowded, to the point you are moving along in a huge mass of people and kind of "forced" along past things by the sheer size of the crowd, so be aware of that and hang onto the kids if it's one of those days. The earlier you go, the better -- I'd be there before it opens. Ticket lines can also be extremely long -- see if you can get them in advance so you can walk straight into the building and avoid the ticket line.
Be careful about Baltimore hotel locations. Like DC, Baltimore is a great town with some very bad areas. Look on TripAdvisor.com for hotel reviews regarding locations. Super-cheap probably means not in a great area. There are big chains right by the popular Inner Harbor area near the aquarium (Days Inn is one) but I don't know about rates in that area. Baltimore is fantastic -- the Maryland Zoo there is very good (has animals DC's doesn't), there are museums about Babe Ruth and Edgar Allan Poe...There is a "children's museum" that is less a museum than a play place but the kids might like it and it's near the aquarium....Look in your AAA travel guide!