once you have iBooks app installed, just drag the PDFs you want onto the iTunes icon. iTunes will automatically put them in the iBook PDF section and you will see a "bookshelf" full of them next time you sync the iPad.
My wife used to print out pages and pages of Real Estate listings to bring to clients, now she just prints to PDF, drags them to iTunes, syncs and goes out the door with zero papers. Clients dig it.