Your process seems to be fine. As you have mentioned, KUKA|prc is using X as the tool axis - it can be changed to Z through an undocumented setting, but is not recommended.
However, no matter how the tool axis is set, the simulation and the movement of the actual robot should always match. It can only match if the tool and base values are the same, see http://forum.robotsinarchitecture.org/index.php/topic,115.0.html
So first you enter your tool XYZABC values in the Custom Tool and check the simulation. If the tool axis if off, you have got two approaches:
You either calibrate your tool for the X-axis, or you rotate your planes.
I wouldn't recommend using different tool values (e.g. always B + 90°) in the KUKA|prc Custom Tool and the actual robot as you have to constantly remember it whenever you make changes.
Hope the clears it somehow up!