Apple has changed the PDF legacy for good. Take the program Preview. Unless a file is protected, you can add text or simple shapes as well as highlight or underline important sections of a file. You can also add notes which is nice if you are reviewing an article. Preview is also pretty good at character recognition, so you can copy sections of a document and past them elsewhere.
Pages, Apple's word processor, is an even more powerful way change up a PDF. It takes far more work, but the results are proportionately more aesthetically pleasing. With this program, you first must open a blank canvas from the template chooser. You can find this option under Page Layout (see the picture below).
Make sure that you have several blank pages ready before you start. Its easier to delete extra pages than to create a few new blank ones.
Next, just click, drag and drop a page from your PDF onto one of the blank pages you've just prepared. It will appear small and off center, but that's easy to fix as I'll explain in a moment.
The PDF will be outlined in blue and have small handlebars (little white boxes) surrounding it. That shows that it's selected and you can work with it. Now open inspector. In the illustration below, it is labeled with the numer 1.
Once inspector opens, click on the Metrics option (#2). For Size, type in a width of 8.5". As long as the Constrain proportions box is checked, the PDF will grow to a hight of 11". With that, your PDF is the proper size (#3).
Now you just need to change the position. Don't try to do this manually. By default, it's put into the background, so you can't grab and move the thing. Instead, use the Position indicators to adjust the placement (#4)
What you're left with is essentially a blank word processing document that has the original PDF in the background. Now you can make all sorts of useful changes. Cover up unwanted content with white squares. Fill in blanks using text boxes. Add pictures or other art. The possibilities are only limited by your creativity.
If you want to keep the PDF format, no problem. Just hit print. Apple gives you the option to save anything as a PDF that you would be able to send to a printer.