The ardupilot site (ardupilot.com) lists both "Mission Planner" and "APM Planner 2.0" with no explanation as to which one to use or how they differ. What are these different options, and where is that documented?
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2.0 is the future, will provide true multiplatform (win,mac,linux) , no awful .net
but it's still beta, some features are already best on 2.0 , I suggest you test both, but use 1.x mainly for first time configuration
APM Planner 2.0 is a beta currently and I think is intended to replace Mission Planner (1.x). The beta doesn't have all the features yet and is still in testing. There is a thread announcing it and asking for feedback.