It will partly depend on what PDF capable app that you've got on your iPad. If want to transfer PDFs into the free iBooks app, then in your library on your computer's iTunes library you should see a Books section on the left-hand side similar to Music, Films, Podcasts etc (if it doesn't show then tick it on the General tab in Edit > Preferences). You can then add PDFs to iTunes via File > Add File to Library, or by dragging an dropping - this may not work if the PDF has some sort of digital rights management that iBooks doesn't support. To get them onto your iPad you can then either drag them across from the Books library over and onto the iPad (which is what I do as I manually manage all my content), or you can set up the type of syncing you want via the iPad device's Books tab.
Other ways of PDFs onto your iPad are via the file sharing section at the bottom of the iPad's apps tab in your computer's iTunes (assuming that your PDF app supports file sharing). Some apps also support transfer via your wifi network from your computer to iPad.