In the Configuration window, click the Game Configuration tab. Select the game in the drop down box, then in the upper right corner of the window that comes up, click Startup. Click Insert on the window that comes up to add a new entry to the startup sequence. Click on "New Entry". Rename the entry to whatever you like, "Console" is always good. Then enter the bind command as you would have typed it:
bind console F12 console toggle
As an example
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