Well I use the longest lasting box that I have the most resources on hand to make. I got almost a whole stack of Blusher Mushrooms Flakes so I think I usually end up with Lucky Mushroom Box (24 hour). During the day I try to seed the low level mushrooms, and at bedtime I put in the high level mushrooms. Once I get around to familiar moon phases I'll probably switch to higher yield boxes. The day I did low level mushrooms all day I found that a grueling day.

I'd stick with going for the hr boxes unless you can find one that your resources match up better with. Wood is the limiting factor, and hr boxes don't use up any more wood then a single use. So except for planning to optimize your harvests, there is no downside to using an hr box over a single use of the same kind. As a dumb perk I found to hr boxes, if I have an hour box going and I forgot to check what substrate was in it and it happens to still have time on it, I can check or double check what the substrate was by checking the box right away. Of course once research is over that is not a perk anymore. Hour boxes are a little annoying if you are obsessive about maximizing effectiveness, but even so, not getting back in time to get the harvest is still more efficient or as efficient as doing single use boxes.