You need an App to view the PDF files. On an iPod Touch I highly recommend purchasing GoodReader. It does a very good job of making PDF documents readable on the smaller iPod Touch screen. I actually keep copies of my car's owner's manual on my iPod Touch and use it over the real thing via GoodReader. I can do this because GoodReader has the ability to "Reflow" the text at a larger more readable font, or it can present the page exactly as it exists in the PDF document.
GoodReader has it is own way to transfer files built in.
GoodReader can also transfer PDF files via iTunes -> Your iPod Touch -> Apps tab. At the bottom of the Apps list you will see a list of Apps under File Sharing that you can drag and drop file on to have those files sync'ed with your iPod Touch via iTunes.
Apple's iBooks can also read PDF and those can be transferred via the iTunes -> Books tab, however, iBooks cannot reflow the text so it is not as easy to read them on an iPod Touch.