Why are there duplicated registers and which ones should I use?

The 0x6*** and the 0x2*** can be seen as duplicates with the only difference being the units. The 0x6*** are the registers as determined by the CANopen standard while the 0x2*** are our own OEM registers. For EtherCAT, you can use either of them as they are connected internally so the unit transformation will be done automatically.