The Sixth Floor Museum is inside the Texas School Book Depository building. The entrance is on Houston Street and is clearly and prominently labeled, so you don't have to worry about stumbling into somebody's office.
The JFK Memorial is just a few blocks from the Texas School Book Depository building, so it's an easy walk -- I suggest leaving your car parked at the museum if you drove there. From the Texas School Book Depository, go south on Houston Street. If you have just left the Sixth Floor Museum or you are standing in the parking lot of the museum, turn right onto Houston Street. Cross Elm Street at the light and walk one block to Main Street. Cross Main Street to the side with the Old Red Courthouse and turn left. The JFK Memorial is the large white monument just past Old Red.
This photo gallery has pictures of the significant buildings and landmarks surrounding the assassination of President Kennedy. The Texas School Book Depository is a rather unassuming building, so it might help to know what you're looking for before you get here.