Neither should be proud, I have removed and re-fitted mine today in another frame, they were a bugger to remove because the spacer tube was a little too wide so I couldn't get my bashing tube to contact with the inner face of the bearings/cups to knock them out after I had removed the crank arms and spindle. Got them out eventually thogh. When I re-fitted them, the bearings/cups went in with very light copper hammer use. The BB shell on the new frame was a gnat's wider so when the cranks went back in, the spacer had just a little movement in it before the spindle went through, so next time they come off, I will be able to knock them out easily. The bearings are now flush within the cups, the cups are flush to the frame. All good.
Is it your cup or bearing that is proud? If it is a bearing then your spacer tube is too long. Take a little off (the amount that the bearing is proud) using file or grinder.
