1.) For some images the watermark is much too big, for some too small. How can I create one whose size is always the same, relative to the size of the image?
2.) The watermark is not always created as the top layer, thus altering the result. How can I make sure that the watermark is always at the top, regardless of which layer is selected in the saved document?
1) Photoshop does not have a scale command where you can enter the percentage of a page. The best help I can offer is view >> new guide >> and input 90% horizontal (do 1 more hor adn 2 more vertical to get a box). You would then have to manually scale to get the layer to fit inside the box.
2)Record Shift Ctrl J or the bring to front command into your action.