Yes, that's the way I did it before I got my long arm. There are many different ways to join the quilted sections. Some are all by machine, some a machine-hand combo. There's a good book by Marti Michell that details several different methods, or you can google 'quilt as you go' to see different techniques.
http://www.amazon.com/Marti-Michell-...ng+in+sections