JavaScript has no effect on printing other than you can call the browser's print dialogue in some cases.
Print CSS may help, but even that isn't fully supported or consistent across all browsers (cough IE cough)
If you want to retain absolute control of the printed piece, this is one of the few instances where I'd recommend PDFs. Have your PRINT link on your web page make a call back to the server, regrab the data, and then format in a PDF and stream back to the browser.