I extrapolated from this post: http://forum.arduino.cc/index.php/topic,68200.0.html, that high current consuming LEDs should be PWMed with a driver.
No that said that high current LEDs need a constant current supply and not just a resistor limiting the current.
It is my belief that the transformer in my system also contains a LED driver but since the system is modular the connection between the transformer and LEDs can be easily disconnected (it is at this location where I would like to add a LED PWM-Capable Driver).
If that is true then you will need another power supply and a constant current driver that you can apply PWM to.