It sounds as if you have a body mesh and a head mesh, with holes ready to connect. Select both mesh objects. Go to mesh>combine with both selected. This will, as it says, combine the meshes... BUT... it doesn't connect them. You do that yourself. If you modeled it correctly there should be x vertices at the bottom of the head, and x (being the same as the previous x) vertices at the top of the body. Select a corresponding vertice set and edit mesh>merge or merge to center, and repeat for each set; OR select a corresponding edge set, and Edit Mesh > Bridge... etc. That will make an entirely new face in between the edges selected. I would suggest the first method w/ merge to center, but I'm not a pro like some of the others out there. Good luck. Lets see some pics, yes?