You can add watermarks in Aperture, but you cannot create watermark images with alpa channel and transparency. For that you will need an external editor.
Any photo editor that understands transparency will do, Photoshop, Pixelmator, the free Gimp, or simply Preview. To create a text watermark in Preview see for example this thread:
You add the Watermark on export, by editing the export preset to include the watermark image.
For plug-ins see: Adding Copyright Symbol & Signature
And for adding the watermark on export see: Working with Export Presets - scroll down to
"To add a watermark image to your exported images"
- Select the images you want to export.
- Choose File > Export > Versions (or press Command-Shift-E).
- In the dialog that appears, choose Edit from the Export Preset pop-up menu.
- In the Image Export dialog, select the export preset you want to use to export your images.
- Select the Show Watermark checkbox.
- Click the Choose Image button.
- Select the image you want to use as a watermark, then click Choose.
- Specify where you want the watermark to appear on the image using the Position pop-up menu.
- To adjust the opacity of the watermark, drag the Opacity slider to a new position.
- If you want the watermark to be scaled in proportion to the image’s output size, select the “Scale watermark” checkbox.
- When you’re satisfied with how your watermark appears in the watermark preview area, click OK.
- Navigate to the location where you want the exported images placed.
- Choose a name format for your exported files from the Name Format pop-up menu.
- Click Export Versions.
Your files are exported with the watermark you created.