If the pots work backwards, I think that just means you soldered the wires on the opposite lugs.
The way a pot works is that the center lug is always "on" or "open". The knob on the top is attached to a sweeper on the inside that... basically, the knob determines how much the left and right lug are connected to the center one. So when it is halfway (on a linear taper pot, audio is different- that is something else though. You can ignore this parenthetical), the center lug is 50% connected to the right lug and 50% connected to the left lug. If it is turned 3/4 to the right, it is 75% connected to the right lug and 25% connected to the left lug. If it is all the way to the right, it is, in theory, 100% connected to the right lug and 0% connected to the left lug. You can extrapolate from there.
I hope that explanation helps with understanding what is happening with the pots. If you want to understand better, open up a spare/old pot by peeling back the tabs and take a look at the inside. It is a pretty simple concept if you can visualize it.
So, if my quick thinking is correct, if your knobs are wired backwards that means what you soldered on the right lug should have gone on the left, and visa versa.
Also, it is better to think of wiring as controlling the "flow" of electricity, because the color of the wires, obviously, doesn't mean anything. You want to trace the "positive"*** flow of electrons and make sure that they go through the different components the way you want them to. Anything that touches anything that is connected to the ground will be grounded out, aka silent. So if you use that thinking, go through and make sure that when you turn your knob that it connects you positive*** flow in varying percentages to what is going to ground, whether that is a wire to the back of the pot on the other lug, a wire going to the negative lug on the jack, or a capacitor that is bleeding the treble frequencies to ground.
***There really isn't a "positive" or "negative" flow in a guitar from what I understand because it is an alternating current, so it is switching between the two rather rapidly. What is more, back when they were laying down the terms and stuff for electrical engineering they labeled the flow of electrons as being positive, but since electrons are negative it is really a negative flow. From what I understand, they left it like that because it had been in use for so long beforehand, and it really doesn't affect the formulae or anything on the theoretical side. This info isn't useful or necessary for guitars, but I don't like giving out half truths that could complicate things down the road if you try to do more complex stuff.