First Step of Transceiver Design

Yes, transceiver dedicated input and output pins must be connected to transceiver PHY IP Cores such as Stratix V Native PHY IP Core. You can find the IP core in IP catalog tool in Quartus II software. I recommend the design flow on alterawiki.com as your first step.

http://www.alterawiki.com/wiki/transceiver_design_flow

You may see a GUI called MegaWizard in the design flow, but Altera has terminated MegaWizard tool. IP catalog is the replacement. No worry, look and feel are almost same as MegaWizard.

One thing you need to be noted is that the transceiver has minimum data rate spec (660 Mbps, 1G bps etc.). Check the datasheet for your target device.