1) dwarves wont use bins to store stuff in stockpiles (have 8 empty bins in my furniture stockpile) but my finished goods stockpile is full of items not in bins(as is my weapons and armor stock).
Check the stockpile settings (
q) on the finished goods stockpile. Make sure bins are allowed, and make sure it is
not set to take only from links. It should be set to take from anywhere.
Meanwhile, look at the bins that are sitting in the furniture stockpile. If they have a (#nn) in their descriptions, then they are assigned to the stockpiles that have those numbers, and simply haven't been hauled there yet.
Finally, note that only
one empty bin at a time will be assigned to a stockpile, in general. So, your goods stockpile might have one empty bin assigned, which is being hauled to it already. Or, the empty bin was hauled there, and then after it arrived, a dwarf grabbed it and is running around gathering up goods with it, after which it will be returned to the stockpile.
it was the same with my cloth stock pile 'till i purchased some cloth (1 full bin of ropereed cloth) from the elves and now all my cloth is in that 1 bin
Hmm... not enough information here.
2) some stock piles are not being used at all. (animal stockpile has none of the filled or empty cages in it and i have plenty of both)
Again, make sure the stockpile is set to accept items from anywhere. It's really easy to accidentally hit
a while looking at a stockpile, which toggles it into "accept only from links" mode, without noticing.
3) have a tame animal in a cage, but i cant get it out
There are lots of ways to remove a tame animal from a cage. The easiest is to designate a pasture zone somewhere, and then assign the animal to the pasture. The second easiest is to construct the cage as a building, then
q it and un-assign the animal.