Since 0.0.3, marking a slot to not be stored via left click now works. Unfortunately it doesn't presently work with the three quick slots added by EAQS (it acts as though alt is not held, instead simply picking up the item the same as a plain left click).
It would be great if QuickerStack worked with these slots, as the original QuickStack does; they're quite useful in particular for storing different arrow types and switching them easily - being able to exclude these slots from storage means we can easily store excess arrows that overflow to the general inventory via QuickerStack, without storing those we're actually using.