The scratchpad isn't intended for keeping track of the words you put in it--that's why it's called the scratchpad. If you want to keep track of them, then add them to another list, then use that list's "Study in Scratchpad" action to get them into the scratchpad.

If you wanted to repeatedly study a set of words repeatedly with progress tracking on, you would just study that section or short list by itself; don't need scratchpad there.