First you need to make sure the two parts of your model are the same object. to do this, select both pieces and combine polygons. use snap by pressing V to make sure the vertices are on top of one another. If they still aren't merging you need to open the option box and increase the distance, but only by a tiny bit. If you are using extrude face and your vertices aren't merged, open up the tool option box under the polygon menu and select keep faces together.

As for your second question. no, you can keep everything seperate.