Phase Correct PWM library?

Im sorry I should have been more clear on what im acually trying to do and what im talking about.

Yes i am making a serial based motor controller along with battery managment sytem using an Arduino and STM l293E. The plan is to connect the l293E to an atmega168 running on an internal 8mhz oscillator, the atmega168 will be handeling battery managment via its analog pins. For motor control the plan is to have the atmega except commands from any serial communication source such as, Forward, Reverse, 45degree turn etc etc. When the arduino recives a serial command via a PC/Propeller Micro/Bluetooth module whatever, it should call a function using an interput. The motors im using also have encoders so I want to be able to have the option to use a closed loop feedback system to do a PID loop on the motors, or switch modes to open control with no error detection or speed compensation on the motors. All this stuff is a little down the line though...

Right now I have an arduino rbbk connected to my h bridge which is connected to two motors. Obviously changing the direction of the motors is no big deal thats just setting certain pins on the arduino Hi and Low which, which are connected to the hbridge chips inputs. Right now all im trying to do is generate two different PWM signal lines using timer zeron, pins 5 and 6 correct? Bit banging PWM is fairly straight forward but one PWM locks up the whole micro to the task, so I obviously wont be able to generate two simaltanous PWM lines while monitoring batteries and serial and all that good stuff.

I googled around about how to use the arduinos timers for PWM generation and found this article http://arduino.cc/en/Tutorial/SecretsOfArduinoPWM. It goes over three different way of using arduino for PWM, there is bit banging, Counter Based Fast PWM, and finally counter based Phase Correct PWM. Being farily new to the Arduino I dont understand the examples it looks as if there or'ing some flags to set a register or something... Im not real sure how to set the PWM frequency either.. I was hoping maybe there is a library using the fast pwm or phase correct pwm methods descrided in that article to dumb it down to something like this

startPWM(pin, frequency, duty cycle);

My hbridge is capable of 100khz signals, from what I know about motor control 200Khz is going to be a really nice PWM ramp for DC motor applications, if I cant use the Arduino to generate pwm frequency this hi thats OK, but I dont see why not, A propeller can do clock lines up to 125mhz and its only an 80mhz chip, so im assuming 100khz should be failry easy for a 16 or even 8mhz chip