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Go into desktop mode.
Click on the Steam icon on the panel and select Library (Steam seems to struggle to open the configurator window without that window being open already).
Click on the Steam icon on the panel and select Settings.
Click on Controller, then click on Desktop Configuration.
That will open up a Big Picture Mode-style window that will let you configure which buttons get used for what in desktop mode. Currently, those don't line up well with the image of the Steam Deck - they're aligned to the Steam Controller - but apparently a less janky version is on its way.
Set up the buttons how you want them. I use right trigger as left click, left trigger as right click, both left stick and left touchpad as scroll wheel, and L3 (clicking in the left stick) as middle click.
That sounds like this part:
It's expecting that the input will go into the new window, but it hasn't opened the new window, so inputs don't go anywhere. If you open the library first, it seems to not get confused.