FPGA design is usually a bit more complex given that there are so many options available, depending on what you want to accomplish. Here are some of the main things to look at:
1) Determine the bank allocation as far as voltages and anything else that might be needed for your board. Altera Quartus II is good for giving you a pin layout (look at pin planner tool) so you know what the capabilities of each pin are and so you can decide the voltage and use of each pin.
2) You can use the altera tools to get an idea of current draw. Note that FPGAs are notorious power hogs (especially at startup peak and with many I/Os driven) and you need to be quite conservative in this sense.
3) Find a reference design for the 3C25 part. Altera has several reference boards and schematics. Scrutinize them for their recommendation of power regulation parts to ensure proper power. Same for clocks.
4) Find or create the Eagle footprint. Altera has some guidelines I believe, though it is better to obtain something already made. Since the part you need is QFP, it's not as bad as BGA. Make sure to look for footprints that might be for other parts but are equivalent (pin, pitch, other specs should be the same).
5) Create or find footprints for other parts and finalize the schematic.
6) PCB layout is usually critical for high speed, and BGAs can be difficult to fan out (especially since eagle isn't much help here). QFP not so much. Read the Altera app notes (and look at the reference design PCBs) to place the capacitors as close as possible for proper decoupling. This is critical.
You can find Cyclone III documentation on this page.
In device handbook, look for "Table 1-2" (p.16). This table shows all available vertical migration options for Cyclone III family. "Vertical migration" means that when you design your board for one particular FPGA, you can replace this fpga with a higher density one (which has all the same pin layout etc.).
According to this table for E144 package EP3C5 and EP3C25 are compatible so you can use device symbol for EP3C5 instead of EP3C25.
Best Answer
Eagle comes with an ULP for this. It's called "make-symbol-device-package-bsdl.ulp" .
Open a new library file. From menu click File->Run, select make-symbol-device-package-bsdl.ulp . Click Browse, find your *.bsdl file. Rest should be easy..