I use it extensively. It's easy.
1. Create your watermark in any program you want (I usually choose Photoshop). Make sure you save it as a png (I choose this because it's lossless) and make sure you have a transparent background.
2. In Aperture, select a photo you've edited/imported into your workspace. Go to File -> Export -> Version. There will be a filesystem browser and some window menus.
3. Go to Export Presets -> Edit. Select, let's say JPEG - Original Size. On the right side of the menu there will be Show Watermark. Click that check box to turn it on. Then change the position anywhere you want. Finally, click the button called Choose Image... There you select the watermark image you created in Step 1. You can choose to scale the watermark or change its opacity as well, by selecting the Scale watermark button and using the slider.
Just play around with it a bit. You may want to have a transparent border around your watermark file (you'll see what I mean when you play with it). You may also have to resize your watermark file depending on how large the files you export are (resolution-wise). That's pretty much it. Every time you export a version of your photo, just select that image export preset and your watermark will be displayed using the settings you made in step 3.
Hopefully that makes sense.