If you find yourself playing the organ without a new goal in mind, you should stop right away and think what you would like to accomplish today. It is very important thing to do. Without this small goal for today your organ practice will not be effective and efficient.
You must have clearly defined goals. For example, this could be just perfecting previously mastered material, learning a new episode of organ music, memorizing one section of your piece and so on. When you have your goal that next step is to take action. Every action on your organ bench will lead you closer to your goal so if your goal for today is to memorize four measures of your organ piece then that's what you have to do.
Don't sight-read any organ music; don't play any of your favorite hymns. Instead you should focus on memorizing those four measures. The best way to memorize these four measures is to subdivide them into for separate measures and memorize them individually. When you can play each of the four measures separately, combine them into fragments of two measures and later of three measures and only then attempt to play four measures without stopping from memory.
So this kind of practice is very specific and helps you to use your practice time efficiently. If you only have 15 minutes available for your organ practice today, don't despair - you still can achieve some important tasks.
For example, you would perfect your previously mastered material that you played the day before. This might mean repeating it at least three times. Aim for correct notes, rhythms, ornaments, fingering, pedaling, articulation, and hand and feet position in each repetition. If you make any mistakes, go back and try to correct them.
Apply these tips in your practice and remember that you always have to have clearly defined goals for each practice session. This will prevent you from using your time inefficiently.