Salem

Is there an option or 3rd party tool to manipulate placement of storage?
Is it possible to put one box on top of other?

There are 3rd party tools that make it easier to place stuff, find here viewforum.php?f=11
But it's impossible to alter the game's physics. You'll have to figure out how to make them work best for you with limited possibilities. Including other types of storage.

FYI the default client (and any derivative) allows you to 'ghost' an object you're carring. While the object is overhead, rightclick it. This will bring up a 'ghost' of the object akin to when building it for the first time.
(If you didn't know about this, be sure to give the How to UI thread a glance. There might be other time-saving stuff in there you don't know about yet).

Do keep in mind, as Yes posted above, that (nearly) all objects have a hitbox (and for that matter, all storage containers do). It's not possible to place two objects so that their hitboxes overlap. For some items, notably chests, hitboxes are not always obviously visible. For e.g. crates the hitboxes coincide exactly with what you see, and there are some pictures around of people placing them rather efficiently indeed.

BTW is there a compass?
Or any type of tool for orientation on map?

Up is North on the minimap. No other tools, I think.

if you are realy needing to know what is noth on main map make a makeshift fence starter corner and then click on it to get your cardinal dirrections from the extend fence north build board,

CTRL-click on the minimap to go towards the point you clicked. Knowing where north is on the minimap you will find your directions.