We currently have Cost + PST + different markups for A-E in Markup Percent. With the HST coming into effect, is there a way to change all of the item's mark up percentages at once, instead of each item individually?

You could export them to a spreadsheet, make the necessary changes and then import the changes.

Could we get some guidance on how to go about exporting all of our items to a spreadsheet and changing the mark up percents and then importing them back into OE? File Format automatically says - ASCII CSV (Delimited) - Leave as that? Field Selection - Markup Factor? Selected Field - Item #? After we export them to the spreadsheet, how do you change the mark up percents there?

You want training on how to use Excel? Import/Exports are covered in the Fundamentals manual.