Triple Speed Ethernet with Cyclone III DSP Development Kit

Have a look at the TSE datasheet, you have a list of registers. You should at least put it in gigabit mode, set up a mac address and a few other things.

The timing constraints are mandatory at those speeds. You must constraint the GMII I/O or you'll have problems.

The PHY is supposed to be properly initialized, but you can still read its MDIO registers through the TSE MAC to check that it detected the link and negotiated the correct speed.