Since I started my book-keeping business I've set my clients up on standing orders in order to get paid. I was chatting to a local accountant who uses direct debits to bill his clients. The set up costs seem high at just over £1,000 + vat, plus a 1% processing fee, but it does offer the flexibility to change the amounts charged easier than with standing orders.
Has anyone here used a DD system to run their billing system?
I looked at it a few months back, and didn't think I would be able to persuade enough clients to adopt it. I think you would need a high client base to make it worthwhile to cover the setup costs and trans fees you mention.