The beta teams have the controllers and are working with both environments. They are anxious to answer all of the questions you have so I'd suggest starting here:
http://forums.usfirst.org/forumdisplay.php?f=743
You will get both programming environments. They both have full download utilities to get your code onto the robot and it doesn't require FTP unless you want to do it that way. The IDEs themselves have a "run" button inside them that will compile your code, automatically download it over wireless, and start it going.