Hi shaul dorf,
Actually, if the chip using the same reference manual ,then the register configuration is the same.

From the above picture, you will get that MK64FN1M0VLL12 should refer to this document, the reference manual which you are referring is correct.
If you want to choose the MUX, and don't know which alternative chip-specific mean, please refer to page 246, 10.3.1 K64 Signal Multiplexing and Pin Assignments, here you will get the detail ALTn function.

Wish it helps you!
Have a great day,
Jingjing
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