Assuming you mean Western Arlington near 50, not Courthouse/Rosslyn near 50, I recommend this: http://goo.gl/maps/9UHdL
Get to 2nd St S and Courthouse, go through Fort Myer (need a photo ID), leave via one of the Henderson Hall gates, which will put you on Southgate. Either stay on the Washington Blvd “trail” (North side of the street) or just take the lane on Columbia Pike and you’ll go into the Pentagon parking lot. Wrap around to the visitors entrance.
Full disclosure: I just bike most of this (to the parking lot) in reverse yesterday. I’m not familiar with the last part, but it doesn’t seem hard to just follow the roads and listen to/ask guards when you see them.