AutBar has no control over what gets used. Blizzard code decides...

hrm... The /use command always uses the smallest stack 1st. However autobar always
picks the lowest inventory slot.

Can how it uses the item be modified to the /use command?

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Making all buttons custom macro buttons can in theory be done.  In practice I will 
wait for the API to improve or the code to be fixed by Blizzard.  The reason is 
simple: I am unlikely to write all the code needed to make custom macros behave like 
actual Blizzard buttons.  It is hard enough just getting the current buttons to work.

Meanwhile some things have improved: the tooltip now shows actual charges of the 
item AutoBar will use.  This can aid in manually keeping your low charged items 
first in your bags.  This is lame but there you go.  If you know of a way to figure 
out the charges on an item and have code for it I can have AutoBar shuffle items 
around so it in effect does the right thing.

I made a small addon called Restack that automatically restacks stacks of the same
item so that one or more of the stacks is maxed. So when an item from a bigger stack
is used an item from a smaller one is moved to the bigger one asap. This has the same
effect as if always using an item from a smaller stack. Perhaps this helps. :-)

So of the 2 issues: stacks and charges, 1 is now solved.  Stacks for buttons with 
shuffle enabled are moved around even in combat.  There is no reasonable way to get 
item charges at the moment though.