Place & Route (Noob Question)

place and route is referring to the design inside the FPGA, you can't do the rest of your project with Quartus itself - though you will need to work closely with whoever is doing the board design on the I/O assignments of the FPGA

to do the board you need a schematic/layout package. there are high end tools like Mentor and Cadence or low end tools like Eagle and DipTrace. there should be no problem doing a Cyclone design in a low end tool, but Arria and Stratix designs would probably benefit from some of the features of high end tools - for example HyperLynx signal integrity simulation