The way to create machines with with quality modules is to have the modules in hand, and drag a box with them over the machines. Dragging with right-click removes modules.
It's explained on the mod page, in the mod page images, in the in-game tips, and on the tooltip for the quality modules. I hoped this will be enough places to learn this from.
If you want to place them down with bots, you need to use the "programming" recipes, available in crafting machines.
As for the 20s thing, it happens when you start using the mod for the first on an existing save, or upgraded from some version.
The time it takes is actually a bug in the game which was solved for Factorio 2.0 :)