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Managing linker script nrf53 (nrf connect sdk)?

I'm trying to evaluate the nrf5340 using the PDK. 

I want to port an nrf52(832) application to it and I'm having a lot of trouble understanding how to work with west and the nrf connect sdk in general. But one of my biggest problems is I don't know how to modify the linker script. This application requires our custom bootloader and various other flash regions. 

Is this something that you use the prj.conf file for?

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