The Smithsonians are comprised of multiple Museums in different buildings. We stayed in Cherry Hill RVP and rode in on the Subway to Union Station. From there we took the Duck Tour with our young GD, one day. Then on another weekend when DS and DIL flew in, we bought the 2-day Trolley Tour to see more from the street side.
Then we would get on and off at whatever Museum or Monument and walk a ways before seeing another Museum.
Cherry Hill is great because they have all the Subway maps, City Maps and people who can guide you ahead of time.