The joysticks I am using are basically potentiometers for each axis. I just used a female joystick connector hooked up power (+5v) to the power joystick pins and then hooked the signal pins into the analog inputs. The potentiometers give me between 0-5v depending on their position and therefore give me 0-1023 for analog inputs using analogRead(). You may have to check if the joysticks you are using are standard game port pinouts using a volt-ohm meter.
I ended up having to use a TLC5940 chip to provide extra pwm outputs. Using the TLC5940 arduino library from http://code.google.com/p/tlc5940arduino/
and the forum listing here http://www.arduino.cc/cgi-bin/yabb2/YaBB.pl?num=1218174457
I was able to easily output up to 16 pwms. The TLC5940 can be ordered from TI directly as a sample just to try then buy more if needed. I hooked the PWM outputs from the TLC5940 into h-bridges to then control the dc motors.