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I was trying to clean my laptop, silly me I removed a thermal conductor from top of a processor *not the main one, I believe its just the south bridge), but the thermal compound got disturbed. I put it back on and tunred the machine up. I am posting from it right now, but I am afriad that I have tinkered with the factory settings.

Should I put the thermal compound manually?

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Assuming that there is still some thermal paste on the relevant spot, I think it might be more dangerous to apply more paste - some people suspect that the original MacBook Pro and MacBook models overheated as a result of Apple applying too much thermal paste during system assembly.

In general, I do not think it is necessary to remove heatsinks and other non-user-replaceable components while cleaning a laptop, especially considering the risks. Since your machine is still turning on and booting properly, it is extremely unlikely that you have caused permanent damage.

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Putting too much paste can cause the excess to flow under the cpu and "short" it out. Not all pastes are conductive, but the one's that are (e.g Arctic Silver), can cause this problem. –  Zabba Aug 21 '10 at 18:35
    
I know Artic Silver, I have fried a CPU with it before :P. Fortunately it was just the north bridge that I took off the heatsink from and not the processor. –  Shahzada Hatim Aug 23 '10 at 2:42
    
According to Arctic Silver, none of their products are electrically conductive. Arctic Silver 5 (what most people are probably using) is capacitive though, which can just as easily toast something. –  Shinrai Oct 12 '10 at 15:10
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As long as the compound was soft there should not be a problem, but if it was hard and dried out, I would consider cleaning all the old compound off both surfaces using isopropyl alcohol and applying new compound sparingly to the heat sink before re-assembly

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A damped-with-water cloth also works well to remove the dried out paste. –  Zabba Aug 21 '10 at 18:33
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