interfacing Altera Cyclone 3 FPGA to a peripheral using UART

From what you said I guess you are targeting a CIII starter board: then you can definitely use the HSMC connector.

Any internal signals implemented in fpga logic can be routed to any fpga I/O pin: so you only need a pcb trace going from fpga pin to a board connector pin.

As I remarked before, you possibly need a buffer (TTL or RS232) to interface the wireless module: read the module datasheet and find out if those uart signaling levels are compatible with fpga I/O ports, which are basically LVTTL.

Also check if the wireless module uart requires handshake signals (rts / cts) besides tx and rx: in this case you'll need 4 lines for the interface, 2 inputs and 2 outputs.