So i got some 3 watt LEDs, but they're wired well, backwards.
I don't know if this is intentional or not but I can't figure out how I'm actually supposed to control these things. Every LED I've ever done was by using the PWM pins and attaching it to the positive end of the LED. So how am I supposed to control these things through the negative end? Is that even possible?
I would say that they're the right way around...
You switch the low side of the LED, not the high side, and otherwise it's just the same. Actually, this is generally the preferred way to switch LEDs (and most other things), because low side switches (NPN transistors, N-channel MOSFETs) are cheaper for a given set of specs than high side switches (PNP transistors, P-channel MOSFETs), and easier to control when the voltages involved are higher than the logic levels in use. And any linear constant current driver (ex, AMC7135, which is made for these kind of LEDs) wants to be on the low side too.
You put the positive side on the supply voltage, connect the PWM pin to the negative side, and you can account for the fact that low means on and high means off in software.
I hope you weren't planning to connect those directly to your Arduino output pin, and get anything like 3W through them! Arduino pins are only good for up to 20mA, (40mA max - more can damage the output driver), so you need like a 220 ohm resistor. And at that point, you're not putting any more power through the LED than you would a normal indicator LED, so it won't be any brighter.
You need to use an N-channel MOSFET or NPN transistor to switch the LED, and drive that with your pwm pin (and these typically invert the output, so high once more means on) - and an external power supply if you want to turn more than one channel on at once (it's 1 watt each red/green/blue). Be sure to use appropriate current limiting resistors - these are going to be low values, like a couple of ohms, and you need the 1W resistors. digikey can provide appropriate mosfets (AOI514 is cheap, through hole, and easily able to handle something like this ) and resistors (ebay is often cheaper for resistors and other passives though). Also - those LEDs get hot, and you need to heatsink them if you want them on full brightness for long. Those 1W LEDs are bright 
I probably wont be having them on full brightness. I'm making mood lamps with them. Regular RGB's just weren't cutting it though so i needed something beefier. Thanks for the advice though. Now i just gotta figure out how to retweak the code.