Do you have hardware already on which this has to run? If that's the case then please tell us what that is which PIC and which pins are available.

Having the encoder pins spread across two different port register will slow it down and is not ideal, two adjacent pins on the same port is prefferable. If those pins have IOC capabilities that's one way to skin it.

You say the encoder have 60 pulses, is that 60 pulses per channel (240 edges per cm) or 15 pulses per channel (60 edges)? If it's the former and you're fine with 60 Counts per cm that makes it easier since it's just a mater of sampling channel B on the Rising edge of channel A. No qudrature decoding needed.

I take it you've already figured out how to talk to the AD9833 or is that going to be the follow up question?