Base layer is meant to be the first item you put on. I am an advocate of multiple light layers - as in i'd rather one string type base layer to absorb moisture, one long sleeve thermal base layer, then bib shorts over these and a cycling top over that, or jacket, to ice the cake. A Gillet can be added to this also. The idea being first off that thin layers can be removed and tucked in pockets if you get too warm and second that the base layers are there to absorb sweat but retain heat instead of you going cold as soon as you hit a descent or stop for 5 mins. If it's raining then put a light waterproof jacket over the op of your cycling jersey.
This has taken me quite a few clothing variations to finally get a happy medium. Nothing worse than going out on a cold run only to find it isn't as cold as first thought and your heavy cycling jacket is making you sweat from the core! The end result is the sweat turns cold through minimal ventilation. Same goes for a long ride with insufficient clothing, the result is far from pleasant.
For the above reasons, imo, the base layer/s must go underneath bibs.