You just need to be back on the job you queued as before before clicking "Commence".

If you need a moment to do so --like if you're in combat or crafting at the time-- that's why the DF notification window also has a "Wait" button. It won't wait for long, so you need to be quick about it, but that will momentarily minimize the pop-up to a small box in your notification window. Once you're ready and back on the job you queued with, you can click there to bring the DF notification window back up and click "Commence".