The place to setup direct deposit is a bit hidden in the CRA “My Business Account” page, so here is where you’ll go:
Log into your My Business Account
Click on your “Business Profile” at the top of the page (it will show your company name, not mine)
In the left column, there’s a “Direct Deposit” Section. If direct deposit is set up already, it will show the banking details under each program for GST, Payroll, etc. If it’s not set up, it will say so as it shows below. You’ll have to click on “Manage direct deposit”.
Enter your banking details and you’re done!