Yes, it is easy to have it display at whatever points in the video you wish, say 15 seconds on, then 30 seconds off, or whatever you want. This is also useful if you want to put up a message for a time and then go back to the logo.

The only issue I have right now is with transparent images. For some reason they come out looking distorted, at least on the preview. I've never tried to finish converting the file to see if that is actually true or not. But on the preview, it's like looking at static for some reason. It shouldn't be like that though, so I haven't figured out how to exactly overcome it. That's partially why I like to use a black background across a strip of the bottom, but also because that hides any logos that other sites had previously typed.

As for making it clickable, I do not think this is possible. If it is, I do not know how. Watermarks can be made clickable because what they are actually doing is putting a linked image on top, which the video playing underneath. But once you put something onto the video itself, I do not see how you can make the video clickable. I will do more research on this to see what I can find out, but as of this moment, I dont think it's possible. You could still accomplish this via an embed code, but just not on the video itself.