Ok... I think I've got what you're looking for. This formula will pay anyone in the top 25% of any tournament that you run. If you have 16 players, it will award the top 4 players points of 16 for first, 15 for second, 14 for third, and 13 for fourth. This would be in addition to the point for buying in, any points earned for rebuys and any points for add-ons. The "Help Completed, I think" shows the formula, as well as the entries for the hits, add-ons, etc. The "Help, Proof for formula" shows how TD accounts for the formula.
For the points earned throughout the time, yes it will automatically be saved, but you have to help TD - you have to tell it how to get the information correctly for you. Part one of stats help shows the "refresh stats" window open, but you need to first tell TD how to sort the tournaments. First click on Edit Profiles (arrow on part one). You will want to create a new profile (stats, part two screenshot). Name it as you wish - League name will work if you are not doing seasons. On the part two, I have some notes for you that you will want to take into considerations. Stats part three shows how to get the overall score to show - which I'm assuming that you want to sum up the points. If you want the best 5 tournaments to show, then we can definitely modify it so that it works for that.
If the formula doesn't work for you for any reason, whether it's too tight in points, or just doesn't work on your side, please let me know. If I forgot to address something, speak up and I'll address it. I think I've got it worked out and everything address. Hope this goes smooth for you!