I've seen lots of tutorials on how to do it in Photoshop (I use GIMP ... it's free, holler!), but there is also a quick and easy way to do it in PowerPoint (it's a lot like the way you'd make a blog button - the tutorial I used for mine is here at the amazing Teacher Wife's blog!). PowerPoint isn't as powerful as Photoshop or GIMP, but for people who are used to working with it, using PP can be faster and easier to use.
First, make sure your PowerPoint slide is blank (no text boxes). {P.S. ... I'm working on a Mac with PowerPoint 2008 ... could definitely use an upgrade, but it still works, holler!}
Then insert the picture file you want - I use the same image that I use as my blog button.
Put the button where you want it and re-size to your liking. You can make it more or less transparent (to make it more or less obvious) by selecting the image and adjusting the transparency from the toolbar like this:
Or by selecting the image, right-clicking and choosing "format picture" ...
... then adjusting the transparency from that menu.
While still holding down SHIFT, right click and choose "Save as Picture."
You can choose many different file type - PNG formats still hold any transparency you might have added to the background. JPEGs work too though.
Now, if you want to add the watermark to your TpT preview thumbnails, follow the same steps, but choose images of your products. To do this, take a screen cap of your file's cover and/or any other pages you want to go in the thumbnails. On a Mac, to take a screengrab you just click SHIFT + COMMAND+4 and drag the image you want grabbed. {The product I chose was my "new math" tutorial.}
Once you've saved it, the best thing to do is lower the quality so the file size is small enough for a thumbnail. I do this in Preview. I open the file in Preview, then go to "save as." There, I'm given a choice of the file type -
I choose "JPEG," so I can change the quality.
Then I slide the bar until it's around 50 - 100 KB.
From the upload a new product screen, choose "Upload My Own Images."
Choose the files you created with your watermark, and BOOM! Images you can "pin" from TpT with your watermark on them. They'll not only lead back to your store, but also carry your "brand" across the Inter-webs. :)
Hope this helps!