CROWN CE1000- slips into fault immediately after connection

Here's a link to the service manual from Crown:

http://www.crownaudio.com/media/pdf/legacy/130352-1_10-02_ce1-2_serv_revd.pdf

That particular channel is blown. These are not the easiest units to repair. Given that this is a commercial amp, I would recommend that this unit be brought to an authorized Crown service center for repair. Expect parts cost in the $50 range plus the labor charge.
Dan

It's very likely that the main power amp section has a faulty part on it that is presumably causing an overload. You should check the devices on the main heat sink of the amp section.

for some reason channel one of one of our amps started clipping. i first noticed it with the drum kit but it slowly moved to the vocals as well. i haven't noticed this issue before today. what do i need to adjust to keep it from clipping?

This is a very sophisticated amp and it will turn the fan on at various speeds when it feels the need for it. Of course, if it's running REALLY hot, going into thermal protection and/or posting a fault you might take a look at it to see if it CAN turn (no obstructions).

It runs in response to certain thermal conditions.

If you're happy to have a look inside the amplifier you can disconnect it from the mains (important bit), then take the lid off and have a look. It doesn't hurt to look for components that are obviously at fault, (burnt, bits missing, no longer connected to the board etc). Be advised there will be some charge in the capacitors still so don't go poking around too much.
If you find something clearly not right, if you have the tools and skills then you could replace the component, or send it for repair. Be advised though that sometimes a fault elsewhere may cause a component to fail.

Before asuming it is the power transistors check the power on relay first as mine had the same proble and it was because of the Relay that did not switch on the one channel or amp (remember this is a power amp and consist of two mono amps)

There was never anything mentioned about the 18 yamaha sub in the hook up process

Unfortunately Crown amps are not the easiest to repair as they utilize multiple levels of amplification. Since you saw a flash, a resistor probable smoked, I would recommend that you bring this to an authorized service center.

Dan