6 Arrays of 16 LED's controlled by Arduino

Ok, I looked at charlieplxing, but I dont see how that will help me, I am drawing 0.32Amps for each LED Matrix, thats 320mA. If I try and draw that from the arduino wont it melt or something? I have been looking around the forums and found a few different topics that can relate to what I am trying to do yet have different comments, so maybe using a different explanation will help:

The LED's are all connected in parralel in different sections, 6 to be exact. Each section draws 0.32Amps And only requires a 3.2v Forward voltage, all the LED's are the same. The first thing I need to work out is what power supply to use, do I use something like this: http://dicksmith.com.au/product/M9985/dick-smith-regulated-ac-adaptor-4-5v-12v-dc-2-5a Next I have to figure out how I am going to connect the LED's so they can be controlled by the Arduino, do I connect the LED's to the 5v pin on the Arduino and wire them in parralel with resistors to match the forward voltage ( Do I mak them 90 Ohm each? 5v-3.8v=1.2v 1.2v/0.02A=90Ohms?) then connect the LED's to the ground on the arduino board? Will this draw enough amps to power the LED's and will this overload the Arduino?
Or
Do I use an adaptor socket for the end of the adapter (I dont know what th socket thing is called) to split the Vin and Ground, and instead connect the LED's to this and still keep the Arduino controlling the transistor, but instead use a 410 Ohm resistor (12v-8.2v 8.2v/0.02A=410Ohms?), then also connect the Arduino somehow to the Vin and Ground that was split? Will this work or will both the Arduino and the LED's be drawing the same Amperage and overload the Arduino?

Also, when I am uploading the program to the Arduino how can I make it not run the program unless it is getting powered correctly (Not with the USB Thingy).

Next I also want the LED's arrays to fade in and out, would this be possible with low resources (I dont want to spend 20$ on a capacitor) I havsee LED fading cuircuts but I Dontsee how to implement them with mass amounts of LED's

P.S: If all the Arrays of LED's are on, that draws Almost 2Amps, the adapter can support up to 2.5A I believe, but is that a safe amount to be drawing when A) it is being used in conjuction with the Arduino and B) The LED's are going to be mounted in plastic of plexiglass, yet the Curcuitry will be inside a wood table, will any of it burn?
Oh and sorry about posting the pic incomplete, It was late and I did not have enough time to make it detailed

P.P.S: Any spelling mistakes are made because the reply box was buggig out on my coputr at school, and the keyboard has to b pressed hard so some keys arnt working right