Well conditional comments will certainly help ease your pain and keep things structured. Make style sheets specific to IE etc. I personally like to organize my style sheets into sections such as:

Global styles such as typography etc..

Link Styles

Classes

Layout styles

Utility styles

Then I make a sheet just for IE which is a completely separate file containing ONLY those elements which need tweaking in IE so it is usually a very small file.

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I hate IE 6. Just sayin....