If your current exposure is too short, then close the aperture.... If you are currently printing at f/5.6, then go to f/8. You'll have 16 seconds to work with.
The way I do this is.... first time exposing, I set my timer to 8 seconds then expose the whole thing. Second time, I have my tool ready at the right location, then start the timer for whatever seconds. For this second exposure, here's how I do it exactly.
First, take a large cardboard and put it on my paper to cover it entirely. Turn on the enlarger so I can see the image. Then place the tool at the right place. Shut off the enlarger. Then set the timer.... ready.... GO! (and start the timer). As soon as the light comes on, I slide out the cardboard and start dodging/burning.
There are probably better ways to do it, but this method works for me.