What's the best way to save a .pdf with comments?

I really like the comment features in Acrobat X, but I'm a little stuck on what "Save As" function is the best for .pdfs. For example, I also use the GoodReader App quite a bit on my phone, and I've noticed that they have an option to "flatten" the markups on a file. When exporting the markings will open up just fine in any .pdf reader. I really like that system, but most of the time I need to use my laptop for the keyboard.
With Acrobat X some markups are consistent (mainly the drawing ones), but the annotation ones are not as easy to figure out.
So, what do you guys recommend for which format is best for saving. Essentially, I plan to grade student essays with markup and then e-mail the files back (or, if it is not too time consuming, upload them in GoogleDocs and then share the link). Either way, I'm looking for the best overall way to do it. Any help is greatly appreciated.

I use stamps and text boxes most often. Occasionally I use the text-editing tools in the comments area, but they really don't save well when I flatten the file. Occasionally, I'll add a file to pdf when I need to extensively comment on a certain area of the pdf. Depending upon the comment I'll either use a text file (my preferred choice), an rtf, or pdf.

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