I think a difference between spell and a prayer can be thought of in that a prayer is asking a divine being to intercede in a situation, event, etc. whereas a spell is the practitioner using their own will, life force, connection to the natural energies to focus an intention to create change. This is why many of us who have been around for a time do not use spells often, because when we make that decision to try an affect a change the onus falls directly back on us; versus asking a divine being who can chose to fulfill a prayer or not. I am not saying one is more effective or better than another – though i have my opinion on that 🙂 – what I am saying is that the intention and personal will in a spell, at least in my tradition, is not interceded by a divine force per se.
Caveat: Other witch traditions may be different.