I have done several quilts now with FMQ and only recently got brave enough to use contrasting thread. I do usually try to match the bobbin thread to the back, but do sometimes contrast the front. I did a couple that had a lot of black on black...I hated working on it. I couldn't tell where I'd been or where I was going. Matching thread does hide the mistakes, but can be hard to see.
Use what you like and are comfortable with. Don't worry about crossing over unless you were entering it in a show. No one will know but you anyway. :)