Specify exact pin locations on FPGA
There are two ways of specifying PIN assignment — you can either use PinPlanner or set_location_assignment to specify the PIN along with set_instance_assignment to specify the IO standard.

I recommend you read I/O Management documentation from Altera. But here are few examples:

These are location assignments for 1 GbE RGMII Ethernet Interface:

set_location_assignment PIN_D25 -to eth_tx_clk
set_location_assignment PIN_V6 -to eth_rx_clk
set_location_assignment PIN_D17 -to eth_rx_c
set_location_assignment PIN_G20 -to eth_tx_c
set_location_assignment PIN_M20 -to eth_reset_n
set_location_assignment PIN_E21 -to eth_rx_q[0]
set_location_assignment PIN_E24 -to eth_rx_q[1]
set_location_assignment PIN_E22 -to eth_rx_q[2]
set_location_assignment PIN_F24 -to eth_rx_q[3]
set_location_assignment PIN_J20 -to eth_tx_q[0]
set_location_assignment PIN_C25 -to eth_tx_q[1]
set_location_assignment PIN_G22 -to eth_tx_q[2]
set_location_assignment PIN_G21 -to eth_tx_q[3]

set_instance_assignment -name IO_STANDARD "2.5 V" -to eth_rx_c
set_instance_assignment -name IO_STANDARD "2.5 V" -to eth_tx_c
set_instance_assignment -name IO_STANDARD "2.5 V" -to eth_tx_clk
set_instance_assignment -name IO_STANDARD "2.5 V" -to eth_rx_clk
set_instance_assignment -name IO_STANDARD "2.5 V" -to eth_rx_q
set_instance_assignment -name IO_STANDARD "2.5 V" -to eth_reset_n
set_instance_assignment -name IO_STANDARD "2.5 V" -to eth_tx_q


And here is an LVDS clock input to FPGA:

set_instance_assignment -name IO_STANDARD LVDS -to in_clk_100
set_location_assignment PIN_AJ19 -to in_clk_100
set_location_assignment PIN_AK19 -to "in_clk_100(n)"


Hope it helps. Good Luck!