I think that baptism by water and baptism by spirit are two separate occurrences but are linked. As anonymouz said one can come before the other, not necessarily at the same time.
The two baptisms of John the Baptist and Jesus were two differnt things. Those bapstised by John were as a symbol of repentance, those baptised in Jesus name were in recognition of him as the Messiah, the Son of God. The baptism of the spirit comes as a result of that recognition whether it comes before or after baptism.
@Kate. If you find you are losing your faith but really would like to keep it, try reading a book called Disappointment with God by Philip Yancy. It's excellent for anyone stuggling with their faith and wondering if God is really there or really cares.