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I have a something similar setup and you should be able to do it with the one configuration. Since linuxcnc supports multiple spindles I just made another spindle instance and then used a mux2 component to switch between outputting the axis velocity and spindle velocity to the mesa stepgen.  I think I just used the spindle.1.on signal to switch the mux2 component.  That way when I issue m3 s100 $1 it will run the second spindle at 100 rpm.  There could be some issues keeping position if you switch back and forth between the modes depending on how things are setup.    

In StepConf wizard, the "parallel port" page there is an entry for "parport base address" so set that to 0x2000 and test if the stepper moves.
If not, also try 0x2010 but it would be good to reboot the PC before testing it.

Habe ich das mit der Konfig der mesa Karten richtig verstanden, dass ich zuerst herausfinden muss wieviele Ein- und Ausgänge ich brauche um dann die passende Konfig auf die Karte zu spielen?

Installiere linuxcnc auf den Raspberry und starte einfach pncconf, dann kannst du dir die Mesakarte aussuchen und siehst selber was man braucht.
Du brauchst die Steigung deiner Spindeln (der Hersteller gibt 0.00375mm/schritt an, also vermutlich 1.5 oder 3 mm).
In pncconf werden Takt/Richtung für die Achsen fix vergeben sein, du musst den Pins nur korrekte Achsen zuordnen. Dann noch angeben an welchen Pins welche Endschalter hängen und das war eigentlich schon alles. Also praktisch nur von deiner HAL-Datei abschreiben.
Oder du schaust hier:  linuxcnc.org/docs/html/config/pncconf.html

If the "Emergency Stop" button (red X) does nothing, this is likely an issue in the hal or ini files.

Can you post your hal/ini files here?

Axis should look something like this initially (before estop is released):


 


After Estop is released and before power (Orange button) is on:


 


and after power is on:


 


 

On the stepper driver, the led is green and on the BOB there are 3 red led lights. I have a 36V 11A Stepperonline and a 24V 6A MeanWell power supply. I measured the output of the power supplies and they are working properly. For now, I just connected the X axis to test if the wiring is correctly and to learn to operate LinuxCNC.I also tried with another driver and stepper motor but is the same. Maybe because I didn't connected the Y and Z axis the stepper motor is not moving? Thank you for your time!