Judd - what I do with a scanned document is to produce a text box. In Word (don't bother about the drawing tools) <Insert> <Text box>. You will then get an "Insert picture here" box which completely screws up your document... but don't worry, it'll be sorted.
Draw your text box inside the "Insert pic here" bit, then - here's the clever bit (well, I think so, anyway) - drag your newly-created text box somewhere else on the page. Then click on the original big box and hit delete. You've now got your original document back, with your lovely new text box obscuring a bit of the page.
All you have to do now, is to move your box to the required position, and right click on the margin of the box then select Format Text Box, which allows you to colour and determine its transparency. e.g. yellow and 50%. And there you are, done.
Sounds fearfully complicated, but, honest guv, it's easy: I use this a couple of times a week for annotating scanned stuff.
Hope this helps.
Jim