So how does one configure Chainfire3D the best way possible ? It is easy if you know what you are doing. By default, you want to enable as little as possible.
As stated, you want to enable as little as possible to make apps work the way you want, as the more you enable, the more CPU Chainfire3D will use to do the work.
IMPORTANT #1: Simply enabling all the options is counterproductive, unless you know you need them all.
IMPORTANT #2: Enabling both "Reduce texture quality" and "Unroll textures" is quite a silly thing to do. Read their descriptions, and think about it for a minute
Both options are available because performance-wise, on some hardware one is better, while on other hardware the other is better.
IMPORTANT #3: "Reduce texture size" is NOT compatible with a LOT of apps. If you are seeing weird things, this setting is likely the problem.
(1) When starting out, you simply shouldn't enable anything. When running an app, and it doesn't work as expected, first go into the configuration and see if there is a plugin (only) you can use to make it work better.
(2) If there is no plugin or you are not satisfied with it, try the "Reduce texture quality" option to see if it improves performance. This is the most "compatible" option to use. Though texture memory use is cut in half, often you don't see a big difference (or any difference at all even) in the end-result being displayed on screen.
(3) Alternatively, try the "Unroll textures" option. Be sure to UNcheck the "Reduce texture quality" option when using this.
(4) As last resort, use the "Reduce texture size" option. While this option greatly reduces memory usage and can have an awesome speed improvement as result, it is NOT compatible with a LOT of apps.
(5) If performance is adequate, try enabling the MSAA feature to improve visual quality.
Specifics - Free version
In the free version, you can only configure the "default" settings, so you'll likely be in the Chainfire3D configuration tool a lot. I strongly advise that when you are NOT using Chainfire3D for something specific, you disable all the options. This is better for system performance.
Specifics - Pro version
In the pro version, I strongly advise disabling ALL the options under "default" settings, and ONLY use "per-app" configuration. This will greatly reduce the chance of conflicting settings between different apps, which does actually happen a lot ! It is also the best possible configuration you can have performance-wise.