To interface with an encoder, you will want to use one of the two counters on the PCI-6025E. To interface with the counters, you can use the PFI lines within the spring terminal block. You have access to PFI lines 1 thru 9 on the spring terminal block.
Then, when programming the counter operation, you will configure the counter to look at whatever PFI line you've connected to. There are many shipping examples you can look at. Just reference any counter examples that use the DAQ-STC chip (that is the chip on the PCI-6025E).
If you need a BNC connection you can connect a PFI line to User 1 or User 2 on the spring terminal block. Then you can connect to the BNC of User 1 or User 2. I hope this helps.
Regards,
Todd D.