So, you've got the driver installed, and you want to know how to make the most of it. Let's go through the options one by one.
First up is the "sensitivity" variable. In povohat's readme for the driver, he writes, "if your intention is to replicate your existing QL mouse settings, set this value to your in-game sensitivity and continue to use this sensitivity value in-game." It technically multiplies the sensitivity into the driver before acceleration calculations happen, and then divides it out after the calculations are done. Simply put, keep sensitivity at 1 unless you are coming from Quake Live.
The "Acceleration" variable controls how quickly the mouse sensitivity will go up. Pretty straightforward - the closer to 0, the closer to "no accel/flat sensitivity." It's dependent on your mouse DPI and USB refresh rate, so keep that in mind when changing your hardware/mouse software around. Also note that the Pre-Scales and Post-Scales will change this too! There is an option in the GUI dropdown "Settings" menu that allows you to scale acceleration to maintain the same slope when changing post-scales and pre-scales. I highly recommend checking those options once you have an accel curve that you like.
"Sensitivity Cap" is the glorious variable that determines where acceleration stops kicking in. It's a multiplier of your base sensitivity (post-scale and pre-scale variables), so a cap of "2" means that accel will only double your sens from its slowest. If you want to maintain muscle memory for flicks, you'll want to scale the sensitivity cap with post-scales and pre-scales too (Settings dropdown in the GUI).
"Speed Cap" is a gimmick. I say this because I specifically asked povohat to add it :). If you've ever been in a game with a vehicle that limits you from turning too quickly, that's what the speed cap feels like. I asked for it to see if you could use it to get perfect turning rate circle jumps in Quake. It's really not that useful though.
"Offset" determines how long it will be until mouse acceleration starts to kicks in. You can effectively make the sensitivity flat (no accel) for a short period of time, then let the accel raise it up after that threshold is met. This is nice in theory, but I found that having an offset made it difficult to get used to small changes in the curve. I keep mine at 0, but if you have a curve with a non 0 value that you are happy with, that's quite fine.
"Power" determines the exponent of the curve. If you set it to 2 (the default), acceleration is linear. If you set it to 3, you have a parabola. Personally, I like linear accel, but I did try stuff like 2.5 for a while and enjoyed it. Similar to the offset, I found straying from the default made it harder to adjust to small changes to your accel curve, but there's nothing fundamentally wrong with using non standard values.
"Pre-Scale X"/"Pre-Scale Y" is a flat multiplier on top of everything (separated into horizontal and vertical mouse movements), but it occurs before the acceleration and offset calculations. Changing this has a tendency to change a few other things inconveniently... I recommend using the next values:
"Post-Scale X"/"Post-Scale Y" is what you will change to affect your starting sensitivity before the acceleration kicks in. It also impacts the other variables you will be changing, but not as dramatically as the Pre-Scales, and as seen above there are options to make the important variables scale with changes to your Post-Scale X value. The X value is for left/right, Y is for up/down. If you want to have your horizontal sensitivity the same as your vertical sensitivity, there is a check box under settings to lock Y to X.
"AngleSnapping" allows you to make mouse movements that are close to a right angle be snapped to a right angle - basically it lets you draw horizontal and vertical lines with your mouse easier. I haven't found much use of it in FPS games, so I keep mine at 0.
"Angle" is a rotation of the initial mouse movement before any other calculations are performed. It is there to correct for any oddly placed mouse sensors. If you move your mouse perfectly left/right on your mousepad and see that it isn't moving perfectly left/right on screen, you might want to tweak this value.