Hello Bruno:
Here is some information regarding your questions:
1- If using Processor Expert you can change the memory segments from the CPU properties -> Build Options -> Generate Linker file. Picture below is for a K64FN1M0 target with the 0x40000 offset:

2- What do you mean with UART debugger? Do you mean the fsl_debug_console? If using MQX you cannot remove it but you could simply disable the pins as explained at the end of this thread:
What is the proper UART assignment for using printf with JTAG?
3- The USB_LDD is a legacy Processor Expert component not compatible with the KSDK USB libraries. Instead you should use the fsl_usb_framework component. In the next thread I shared an example project for K64 using this component:
Re: Standalone bare metal USB MSD with K64F, KSDK-1.1.0 and KDS 2.0.0, SDHC and fatfs
I hope this helps clarifying.
Regards!,
Jorge Gonzalez
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