After doing a complete read-through of the piece (which I touched on in my first post on this topic), it's a very helpful next step to identify trouble spots and to mark them in the score. I use brackets, in order to remind myself where the spot begins and ends.
There are several reasons to do this. One, is that you start to get an idea where the parts of the piece are that require more attention, whether it be at or away from the piano. Another upside of doing this is so that if you are short on practice time, you can very easily focus in on the spots that need it most, leaving the rest of the piece for another day. Finally, if I decide to play the piece again down the road a few years, I will have a record of those tricky spots!