I used to. It was applied to gross equity, including interest rates, which was in conflict with my Disc Doc, so I switched into electronic invoicing. Otherwise it worked well. That was 3 years ago - things may have changed by now.
When you used "automatic payment", did IB deduct the fee from your clients capital gain and add the fee as your trading profit in your account in the 1099 tax statement?
Is the management fee taxed as capital gain or revenue for your corporation?