When choosing the correct spring weight. Keep the following bit of information in mind. Just because you are able to achieve 20-25% sag with the springs that are in the fork, doesn't necessarily mean that you are using the optimum spring weight. You will probably be able to achieve proper sag with springs that are too soft for your weight, by using a lot of preload. Likewise, you can also have proper sag on springs that are quite firm, by using zero preload. For example, Marzocchi's standard springs in the Marathon S are for riders weighing between 180-220. If you are 220 pounds, then you will need to really crank down the spring preload adjusters in order to achieve 20-25% sag. However, increasing the preload on the spring only changes the initial force on the spring, which decreases the amount of static sag. Increasing the preload is not changing the actual rate of the spring. This 220 pound rider, would likely complain that they are bottoming the fork out far to easily (or too many times per ride). By switching to Extra-Heavy springs, the 220 pound rider would be able to use less preload to achieve proper sag, but the actual rate of the spring would ramp up far quicker near the end of the fork's travel, eliminating the bottom-out problem.
Let's suppose that we have a rider that needs 32.5 kg in order to "hold up" the rider's weight. We are trying to achieve 30mm of sag. The graph below shows a "soft" spring with lots of preload to achieve 30mm of sag and a "heavier" spring with very little preload at the same 30mm sag point (the X-axis). The Y-Axis shows how preload affects only the initial force required to move the spring. The softer spring crosses the Y-axis at 17.5 kg at zero travel. The firm spring hardly needs any preload and it has 2.5 kg of spring force at zero travel but ramps up much quicker. Therefore, both springs have the same 30mm of sag. However, the effect of the spring rates becomes magnified as the fork moves deeper into its travel. At 90mm of travel, the difference in spring force is over 30 kg of force! Maybe THAT's the reason your fork was bottoming out:)
Obviously, both springs are going the ride very differently. My advice is to experiment with different combinations. Maybe you'll like using stiffer springs with less preload, or maybe you prefer softer springs with more preload.
Bottom Line: Proper spring choice is very important on any fork/shock. If you are not getting full travel out of your Marathon S (or you are bottoming-out too easily), be sure you are on the correct springs for your riding weight before you start messing with oil heights, oil weights, etc. You will save yourself a lot of time and headaches if you do this first! If your riding weight (with gear) is near the extremes of the recommended weight for your spring setup, then it would be a wise investment to purchase the next heavier or lighter spring set (keep in mind that you don't have to change the springs in both sides; you can customize the ride by swapping only one spring too).
Damper settings will always have several compromises involved. There are three ride qualities that you need to consider here- Plushness, Traction, and Perception of Control. The graph below illustrates how these three variables relate to each other and how rebound damping will affect them.
Maximum plushness is achieved with the quickest damper settings. However, this setting will cause your traction and control to suffer. I tend to prefer a setting that is towards the "Maximum Traction" setting because it seems to be a happy medium.
Standard Disclaimer: This site describes my experiences tuning and maintaining my suspension fork and this information is not an instruction manual. As always, use this information at your own risk. I am not in any way responsible for typos, misinformation, or any of your actions or results. Results may vary.