Hi @Lukaz ,
If you need to debug the RT1061, you need the debugger at first.
If you are using the MIMXRT1060-EVKB board, it has the on board debugger directly, you can connect the opensda USB port, then the default debugger is CMSIS-DAP, you can open the SDK project, then debug it directly, the board need to enter the internal boot mode.
If you are using the customer board, you need to find an external debugger, eg, Segger JLINK, then through the SWD to debug the chip project.
We also have the application which may useful to you:
https://www.nxp.com/docs/en/nxp/application-notes/AN12183.pdf
Wish it helps you!
Best Regards,
kerry