don't be disappointed, BB! As DrDave says, better to problem solve now than have to rectify things when there is water and fish in the pond. Consider yourself lucky that we have stopped you in time.
If you had told us about the rocks as part of your plan, we certainly would have stopped you sooner. If your rocks are cemented to the wall now, they should be relatively easy to remove since it is fresh work. Simply take them off and then pass another coat of your waterproofing paint. Perhaps now that there is more room in the can the paint shop can put some more black in it for you. Otherwise your dark brown will be fine, too. As long as the color is very dark you can see the fish well.
You would be shocked as to how many of us have had to re-do things we've done with our ponds. It goes with the territory when you're starting out.
You'll be fine. Just backtrack a bit and undo the rock. Trust what we're saying in that we will be saving you from a headache down the road.