Hello felix.boeckmann@zf.com,
Nice to hear that you are using our toolbox on your custom PCB!
I think there are 2 ways of using our MBDT toolbox on your custom PCB:
1. The easiest way is to use the RappID bootloader. This means that you need to flash the rbf file that comes with our toolbox {AddOns\S32K\Toolboxes\NXP_MBDToolbox_S32K1xx\code\tools\BootLoader\RBF_Files} on the MCU.
After that you need to select in the config block the Serial way of downloading the generated code on the target like in the image attached.

But this bootloader uses the UART 1 pins PTC6/PTC7. What pins have you routed out?
For more info, please have a look on this topic (even it is for MPC5744P, the procedure is the same) https://community.nxp.com/message/1102835?commentID=1102835#comment-1102835
2. If you really want to use the OpenSDA from the EVAL Board, I think you need to consider connecting the pins from J14 (from the EVB schematics) to your custom PCB: RST/DIO/CLK pins. Don't forget about the GND!

But if you connect them directly, now you have two MCUs connected to the same openSDA so you need to break the DIO and CLK signals connection with the MCU from the EVB. You can do this by removing the 0R resistors R122 and R127 according to the S32K144EVB-Schematic, page 3.
Hope this helps you!
Marius