I only wear a base layer during the winter. When I do wear a base layer with bibs, the base layer goes under the straps. The jersey always goes over the straps. Always.

I find it interesting how many people say they will never wear shorts again after wearing bibs. I have a few pairs of each and wear them all. Each has its advantages and disadvantages. I almost always choose the bibs for anything over 50 miles where their main advantage really comes into play. My shorts will sometimes start to slip down, causing friction in my crotch while pedaling. This only happens to me on long rides. Bibs prevent this from happening at all. Shorts are a little cooler on very hot days. Shorts are much more convenient if I need to sit on the porcelain during a ride.