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1. My mobo is an ATX, and my power supply is an EATX. What should I do?
Power supply EATX? I believe your case is EATX which means it will fit a bigger size mainboard..
http://www.pcguide.com/ref/case/formATX-c.html
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2. What colors are positive and negative. I know Black in negative and red is positive, but what about when its green and white, orange and white, and so forth?
Black is Ground, 0V if you will, not negative http://xtronics.com/reference/atx_pinout.htm
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3. I notice that my AMD 64 4000 (socket 939) heat sink came with a little paste on the heatsink it self. Should I buy more, or just leave it like that?
You can leave it like that but it's better to scrape it off and buy some decent heat-paste..
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4. My case came with two wires that are blue. They look like thermoniters. They are connected to I believe its a screen in front. I have the Lian Li PC-7. Where do thos wears go, and how do I tape them there?
Anything in the manual (of your case)?
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5. My computer doesn't turn on, I have 480 watts. Its an ANTEC true blue 480. If any advice possible it would really help. Thanks.............
Sounds like you forgot to connect the powerswitch to the mainboard.. Usually a two wire connector marked "POWER" that needs to be connected.. Look in the mainboard manual where you should connect those...
In case you don't have the mainboard manual, you can usually download it from the manufacture's site.