When you add watermarks to a PDF document, you want them to be visible unobtrusively. The following settings for the Watermark tool in Acrobat (Document > Watermark > Add) work best for me:
Size: Varies. For shorter watermarks like the word Draft, 72 pt works well.
Color: Pure red (R: 255, G: 0, B:0)
Opacity: One notch above zero on the slider (12%)
Location: Appear on top of page
If required, you can specify different watermarks for different sets of pages. Click Page range options in the Add Watermark dialog box to do this.
To understand how you can work with watermarks in Acrobat 9, see this Help article.