Hi Michael, I think I understand what you are asking but I think you are making it more complicated than it needs to be. If you were to have your full res image at say 3500 x 2333, resized this to 1000 x 666, then ran the action to place your watermark, flattening the file would set in place a size ratio for your image/watermark. So if you were to then resize the same image further to 500 x 333, the ratio would stay the same, the image would resize along with the watermark. Is that what you are asking? You can change the size of layers and objects in Photoshop using a "Percentage" too, which I think this may be more towards the answer you are looking for.
I could build you an action that did everything from start to finish that resized the image twice, saving one copy at 1000px wide and another at 500px wide, let me know as it doesn't take long to record and tweak a new action for this. The only problem here is that when you record a "Save" step into an action, the action will include the specific folder you used to save into when you recorded the action, so the next time you want to use it it will always want to save into that same folder.
The work around here would be to utilize the scripting powers built into Image Processor, using it to save, and not the action. This would require the use of two separate actions though and you would have to run Image Processor twice, for each image size.
As to sharpening, I am no scientist or maths expert, but I have spent a lot of time experimenting visually with sharpening and creating various actions for customized sharpening. I never use the "Bicubic Sharper" resampling as it destroys edges and sharpens out of focus areas, and does way to much sharpening without any of my control. A better workflow would be to resize your images using "Bicubic Smoother" and then sharpening your image at its destination size, using Smart Sharpen or any other sharpening method you may prefer.
However, when you record an Image Resize step in an action, you can choose "Bicubic Sharper" and it will use that everytime you run the action.
I hope the above makes sense to you, if you have any input or want to research things further go for it, if you want me to build you an action, let me know what you want it to do, the more specific you can be the better so I can get everything into the action and make sure it preforms well.
Cheers and Enjoy your weekend.