One thing that confused the hell out of me for the longest time was the placement of crates and barrels and such. I'd tell the guys to place a crate somewhere and instead of taking one of the just about to built ones they'd just move one of the already existing crates, contents and all. Eventually I realised that if I wanted them to use the pine crates I was having made then I should select Pine Crates (0) from the menu and hey presto no more apples in the ore store. Another tip for when you're delving too deeply and too greedily is to set a local stockpile of 1 or 2 squares amidst the rock or soil you're collecting and make sure that it has a higher priority than the main stockpile. Your gnomes will gather all the rock/soil up into those two squares and when its gathered you can just undesignate the stockpile and the gnomes will the carry the stacks back to your main stockpile instead of individually. Unfortunately this doesn't work for ore, as soil and rock are the only materials that stack but you can instead have a crate dragged down into the mines and use that for the same purpose as a remote stockpile and carry the entire thing back in one go.