I haven't really had a need for chamois butter - but fellow-riders find it (or something like it)helpful. Applied directly to the shorts.
Sometimes extra thick padding is more irritating/causes sore spots than a thinner pad. Or, different manufacturers and styles of shorts can rub differently. I personally am not comfortable in Pearl Izumi shorts (wish I was!). So you might want to consider another brand.
Rebecca, I'm glad the cotton worked for you....most people find riding with just shorts to be the most comfortable (once they can get over it mentally) - but really it comes down experimenting and finding whatever works!
One tip I've learned is to never ride in shorts twice. That is, always wash 'em in between rides.
One last thought on the subject, as a joke I got my husband (also a road rider) some Anti-Monkey Butt Powder. Here's the link - I found it in my local bike shop: http://www.antimonkeybutt.com/
And now he SWEARS by the stuff. It's got some powdered calamine in it, and it really seems to help with keeping dry and chaff free.
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