not sure i am following your question exactly.
RE: the collision position register usage...this value is set to zero automatically by the decoder at start of receive. The decoder then counts the received bits from zero up and when detecting a collision it triggers an IRQ. The user doesn't have to do anything.
It is possible to manually clear the value by switching from RFID mode to NFC mode and back to RFID mode.
For example writing 0x21 to Reg 0x01 (NFC mode) and then write 0x08 to Reg 0x01 (RFID 14443A).