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Z offset is ignored in SKR mini e3 v2.9

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I finally decided to upgrade my ender 5 pro with the skr mini e3 v2 and the touch screen. Had it bought a while ago. Initially, I choose to use the BLTouch as end-stop, and reconfigured the connection for the probe port. All worked well except that the Z offset is not used. I had to send a m211 S0 to allow for a negative offset, but the value is totally ignored, causing the printer to print a mm above the plate. probing does work. I used the firmware from BTT Github. Next I did the same but have setup all full on the probe port. Not well documented, but I have set the Z end-stop switch into the Z end stop port. Homing the printer does work, and the BL touch is not used. When I level the bed the BL touch is used. The problem: the Z offset. If I reset the EEProm then I can get a decent print. But the printer then works with the mechanical end stop as reference. If I level the bed then the printer prints 'in the air' again. Z offset is ignored. If I use the probe port then it makes sense that the Z-offset is 0. But leveling the bed causes the Z-offset to be <> 0. I hope that someone can answer this. I have watched tons of videos, but ...

I'm am searching for some docs that explain how to setup the BL Touch correctly, Better, how do I enable the Z-offset?

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