Oh my gosh, there are a lot of apps that'll let you annotate your own PDFs. To start:
1) Goodreader ($4.99 USD) - described as the "Swiss Army Knife" of apps cause it'll do way more than just annotate PDFs
2) iAnnotate ($9.99 USD) - the premier PDF annotation app
3) neuAnnotate (FREE!) - pretty robust for a free app
There are oodles more, but this'll give you an idea of the range of products available.
With all of them, you can "Open In..." your PDF (either from email or an online storage or iTunes) to get started.
I'd actually recommend Goodreader, mainly because it IS so versatile. However, give neuAnnotate a try. I've used it and it's quite friendly ... especially if all you want to do is annotate a specific/one PDF.
Good luck.
Marilyn
P.S. And yes, you'll have to use the PDF version of your template - although iAnnotate will convert the .doc file to PDF for viewing and/or annotating...