Wear them however you want, just realize the overwhelming majority of riders who wear cycling shorts NEVER wear anything underneath, and dont get chafing.
I do remember getting it a few times when I started, and I did have to use CB I simply used it directly on the pad and the only sensation I had was a light lotion feel when I took the shorts off. But I take a shower after I ride, so that lasted all of 10 seconds.
After about a month, i dont really use it anymore unless I am doing centuries. They also make a much thicker paste type that applies directly to the skin and thats what I use now (I use hammer brand, but there are many brands)