No you only need to connect it to one input, fortunately! It will be either fed to a pll or routed as a global clock and can be used everywhere inside the fpga. Each clock input pin can be connected to a different clock.
Before you finish the PCB (or even better, before you start routing it) it can be a good idea to make a basic FPGA project with all your pins correctly assigned and run a I/O check from the Quartus pin assignment editor. Just to check you got all the pins right.
