The amount of bacteria in the substrate is pretty negligible compared to what's in the filter media.
That waterbottle method works pretty well for flourite, I've done this exact thing before. If you are using sand, you'll need something with a smaller opening. Another plus is that you don't need to wash it, pretty much all the dust/cloudiness remains within the water in the bottle. It's also great since the substrate grains sorta 'rain' or 'sprinkle' down and spread out a bit, so it works really well for this sort of thing.
I wouldn't bother with any prep work, stick some in a bottle, fill it with water, and sprinkle it out where you want more, remove empty bottle with cloudy water, repeat.