Not quite sure I understand the question, there's a bit of an "Apple vs Orange comparison. "Orbital Mechanics" is about manipulating your Orbit - knowing when to apply how much force in what direction to achieve the desired results. A cockpit is about manipulating the vessel. If you are asking if the cockpit is accurate, not in the "stock" Atlantis. Some add-ons, such as Space Shuttle Ultra (AKA SSU) the cockpit is much more accurate and "functional".
As far as Orbital Mechanics, Orbiter is fairly accurate. Orbiter is based on Newtonian physics, rather than Einstienian, so relativity isn't modeled. However, when travelling in the solar system (unless you are using a very futuristic ship such as the Vespucci-D) you won't be going fast enough for relativity to have any significant impact, so the sim is still very accurate. The methods used to navigate and manuever in Orbiter are the same as used in real life. In real life, however, Mercury exhibits some relatavistic effects - Newtonian physics (gravity, inertia, equal and opposite reactions) don't quite explain Mercury's orbit. These differences are slight, but Orbiter probably isn't as accurate for trips to Mercury as it is for, say, trips to Mars. Also, Orbiter's atmospheric model isn't quite accurate either (Earth's atmosphere is being modelled more accurately in the next vesion) so low orbits around planets/moons with an atmosphere are a bit innacurate also, but the difference is small. In Orbiter, atmosphere's have a hard threshhold above which the atmosphere isn't considered so an Orbit that will be stable in Orbiter may not be IRL. For instance, currently the Earth atmo ends at 200k, so the ISS will remain in Orbit indefinitely. IRL, there's still a very tiny bit of air even that high up, and the ISS will require "boosting" every few years to stay in Orbit.
