I never pay much attention to the payloader tool, and it may be erroneous if you are running mods.
It might be a good idea to get a good grasp of orbital mechanics before you start using mechjeb (particularly as you kind of need to understand most of the terms like prograde, retrograde, Apoapsis, Periapsis, etc).
I know for me, one thing that use to give me lots of headaches coming over from orbiter (aside from the lack of needed information) was trying to understand the nav ball in space (the lack of a cockpit view also did not help me).
Also the newer version finally seemed to add tools to help you calculate orbits in advance and burn values and times. just mouse on your orbiter path (you will see a dot), click, and select add manuver, you will see 6 icons (prograde, retrograde, +/-rad, +/-nml), grab one and drag it away from or towards the circle and it will show you the new orbit changes as you drag. Then let go and it will put a new heading indicator on your ball, aim at it and when the clock reaches zero, burn.
Anyhow found this really good tutorial video for ksp orbital mechanics.
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