Good transportation links. Remeber to bring your own ammenties tea/coffee/water/soap (small shop just down the road if you need).
Use the shuttle - it just makes check in less complicated.
The apartment works as a great springboard to Lisbon hotspots.
Definitely go try Cafe Cristal (<1km walking... Be warned it's up hill but so worth it) . The pastries are always fresh and the local lunch (12-3pm) is tasty and well priced.