You take a -6, because your speed is 20, regardless of the action taken to move or distance actually moved.
Your Jump check is modified by your speed. If your speed is 30 feet then no modifier based on speed applies to the check. If your speed is less than 30 feet, you take a -6 penalty for every 10 feet of speed less than 30 feet. If your speed is greater than 30 feet, you gain a +4 bonus for every 10 feet beyond 30 feet.
You use whatever your speed is. Your speed is a more or less static thing, and is not depending on any specific actions you are taking. For example, your Jump bonus does not go up when you take the Run action, because your speed is still 20ft, you just move 4 times your speed in a single round.
Likewise, charging does not increase your speed, it only changes the amount of distance you cover while still getting to make an attack.
(Unless you have a Feat or something that says "Your speed is increased by 20ft while charging", but I have never heard of such a thing)