When you have it level (or sort of level) mark the holes, drill the top one first (make sure you go straight into the wall to avoid breaking off the bit)
I also found out that putting the top screw in the brace on the wall first before drilling the second hole is a lot easier, it makes it less difficult to keep it level. (But in the picture I had drilled both of the holes, it caused a lot of problems for me because they weren't level even though I tried, it was just harder overall.)
Drill the second hole after re-leveling and put the last screw in.
I found that using just two screws, on the top and bottom holes, works just as well, and it saves on screws. (I only put two on the others bookshelves I made, except on this bookshelf only one screw went through the stud and I put the other through drywall and added the extra, just in case)