1) Do not practice for long periods of time at first. Although you might have used to play the organ for several hours a day, I do not recommend you jump in and resume the practice in the same way. You have to realize that while your motivation and interest in organ might be the same as 10, 20, or 30 years ago, your stamina is not. In addition, your body might not like sitting in the same position for hours. Therefore, I think it is best to expose yourself to organ playing gradually.
Start practicing with just 30 minutes a day. This way you will avoid overexertion which is not very healthy. The most important thing about your practice is that it should be regular. You will achieve more if you practice for 30 minutes every day than for 3 hours just once a week. Of course, with experience you can practice for an hour or even longer but especially long practice sessions should be avoided.
2) Choose easy pieces first. Although after resuming organ playing you might have plans to learn your favorite technically advanced organ pieces, you should be aware of your current technical abilities. Remember that after years without practicing organ your level is not the same anymore. Just because you might have played and learned some advanced level pieces years ago does not mean you will be able to play similar ones right away. Therefore, I suggest you do not pick up your organ practice where you left in the past. Instead, play some shorter and easier compositions at first.
These could be works with thin texture, slower tempo, simple melodic lines and rhythms and long note-values in the pedal part or even manualiter works (without the pedal). Especially suited for this purpose are 8 little preludes and fugues, BWV 553-560 formerly attributed to J.S.Bach, some easier chorale preludes from the Orgelbuchlein, chorale preludes by J.Brahms, slow movements from Mendelssohn sonatas, pieces from L'Organiste by C.Franck, "Practical Organist" by A.Guilmant and other works.
3) Have a goal in mind. In order to resume organ practice successfully, you must also have a dream. This is what keeps you practicing in the first place. Without this goal, it will be difficult for you to learn the pieces that you choose. Instead of focusing on your goal, you might play many different compositions without ever learning them. However, if you truly want to improve your organ playing, having a goal in mind will greatly facilitate your progress.
4) Make a practice schedule. I have noticed from my personal experience that a detailed step-by-step plan is essential in any kind of undertaking. This plan is precisely what helps your dream become a reality. Your plan might include steps in mastering any particular piece that you like. Once you have your plan, create a practice schedule for fulfilling your plan. Be very precise and indicate specific time of the day which you will use for practicing organ.
Your practice time might be the same for every day of the week or you can reserve different times for different days. Whatever you choose, make it constant. Then all you have to do is to stick to your plan and follow your schedule diligently.
Of course, adhering to my suggestions will require some willpower but if you truly want to practice for many years, you will not regret it.
You can also download my FREE video guide: "How to Master Any Organ Composition" in which I will show you my EXACT steps, techniques, and methods that I use to practice, learn and master any piece of organ music.