Try to have the run removing tools at hand before you spray. I like using Nib Files and Run Blockers to remove runs. I allow the urethane to harden for about 8 to 16 hours depending on the temperature and hardener being used then I use the nib file to remove the heavy part of the run. The file can take off a lot of the run material without taking off material around the run. A "coarse" file (shown above) has long teeth that run one side to the other these are used parallel to the run then are angled slightly and the motion of the filing is along the run NOT across it. This will shave off the fresh paint like slicing cheese. This is a moderately slow motion without a lot of pressure especially in the beginning. When the file starts to hit the surrounding paint stop using the file and start using the Run Blockers.
Wrap some 600 wet sandpaper around the Run Blocker (shown below) and sand the run lightly until you start to remove paint around the run then stop. If you are working on paint that is less than 24 hours old you should now wait another 24 hours before continuing. After waiting you should notice that the material that you exposed after this initial sanding has shrunk and has helped you level the surface. Using the Run Blocker again sand a little more using the 600 then switch to 1200 or 1500 to remove the 600 scratches and finish leveling the surface. When the surface is smooth and level you can then buff to bring back the shine.
NOTE: If you are painting and see a run forming be sure to apply some extra paint to that area so that you have more surface material to work with but try not to make the run any worse than it already is. The extra paint will give you a thicker coating to work with and can help eliminate sanding thru the finish. Apply extra paint after the paint has dried a little and remember that the paint will be thinner above the run more so than it is below or around it so go easy sanding on top.
AND... While I recommend this procedure before the paint is fully cured it can also be done after curing but it will be a little more time consuming.