Safety protocol dictates that the crew be fastened securely to their seats while the ship is accelerating. Onboard work stations are fully networked allowing full transfer of control from one crewmember to another in the event of an emergency, an integral function of Windows Vista XT NASA OEM Edition (fictional).
In terms of up and down, you are correct, down would be the opposite direction of the thrust of the ship whether it is the main engines or steering thrusters. However, the "downward" force would only be felt while accelerating. Once the target velocity is achieved, apparent weightlessness resumes. Most present day spacecraft have an initial burn to get them up to speed and then take advantage of the near frictionless medium of space. For most missions, advanced maneuvering is unnecessary.
Keep in mind that these ships were designed without the knowledge of extra-terrestrial life. During the design phase, no accounting was made for the necessity of maneuverability during combat. As you may notice, there are currently no weapons mounted on the ships. Who would they fight? Also, think about the original Star Trek series, most of the movies, and the Next Generation. The ships mostly sat off each other's bows statically taking potshots at each other. Even in Battlestar Galactica, the larger ships remain stationary. Not to say that this is realistic, but it is certainly an acceptable form of combat among sci-fi genres. My intent is that combat between these ships will be carried out by fighters. If you look at the underside of the hulls of the ships you will see drop-out hanger doors.
Anthony, that is exciting to hear that they are at least thinking about a Mars mission. In terms of the reusability of the entire craft, that is definitely the fictional part of these designs. I am more or less clinging to the concept of the Venturestar with its ability to take off and land with minimal turnaround (minus its major design flaw that killed the design). Thanks for the links.