My Dana 44 caps were marked with the letter R. the cap was stamped at one end in the same orientation as a cooresponding mark on differential cover seal surface. One side the "R" stood upright, the other was laying down.
Your second question about bearings has me lost. Are you asking if you should replace the bearings on both left and right sides? If so, I'd say you may as well and why wouldn't you if you had it tore down that far. If you are asking if it matters what bearing goes on which side it doesn't matter - you should be using new bearings. If you asking which way the bearing goes on the carrier. Then, well, I'm not saying this to be mean but there is nothing that would stop you from putting them on backwards except stupidity in which case you should get someone to set them up for you.