The IRS has not answered this question directly.
They have said this:
"The economic impact payment will be deposited directly into the same banking account reflected on the return filed." Economic impact payments: What you need to know
This could be interpreted to mean they will use bank account information from your return to make a deposit, even if it direct debit information.
In the coming weeks, the IRS plans to develop a web-based portal for individuals to provide their banking information to the IRS online, so that individuals can receive payments immediately as opposed to checks in the mail.