Cyclone III pin configuration

The EPCS devices do not support JTAG and you can't use the same pin header for JTAG and EPCS AS programming.

That said, Altera did not go dumb and you don't need to have two pin headers.

You can still program the EPCS via JTAG using JTAG Indirect Programming. First, the FPGA is loaded with a Serial Flash Loader configuration. Then, the EPCS is programmed from JTAG through the FPGA.

Thus, you only need to have pin headers for JTAG.

Yes, MSEL must be set for AS.

Go to http://www.altera.com/literature/lit-cyc3.jsp and check your design against the guidelines.

In particular, double check against the Device Pin Connection Guidelines. There's a lot of more pins that you may or may not have to worry about, depending on your I/Os (VREFs, RDNs, ...).

If you want to use even one PLL, you need to connect all the PLL power pins.

Even if you don't want to use PLLs, I'm not sure it's safe to leave them unconnected. Guidelines say it's not.

BTW, you'll notice that the recommended I/O voltage for JTAG in Cyclone III is 2.5V.

I think it's possible to use 3.3V as well, but if you intend to, best check here in this forum first.

Perform pin assignment and synthesize an empty top level before signing off your PCB for manufacturing to make sure your assignments don't violate any rules.