A long sleeve jersey has zippers and pockets. A long sleeve baselayer is more like a long sleeve undershirt but typically made of a wicking fabric. I usually wear a baselayer underneath something else, and a long sleeve jersey either by itself or over a baselayer. I've also worn baselayers under short sleeve jerseys.

The normal approach to layering is a wicking layer by your skin, then an insulating layer, and finally a wind and rain/snow blocking layer. Sometimes the final two layers are combined in a single garment.

Paul