Regarding AE spatial storage, you don't actually copy the chunks... you cut and paste, never copy.
If you place the spatial chunks in a different place, you swap the new area you marked and the area in the cell. I believe you have to make a new cell if you don't have an empty area to place the full chunks into.
You cannot rotate the stored area; north will still be north.
Remember (or write out) the pylon positioning for your copied area; it must be identical to how it was when you cut the original area.
Using additional pylons to outline the area decreases energy cost for storing a given area.
Also, there were concerns I only vaguely remember regarding tile entities and block metadata, and also some sort of blacklist. Test extensively.
(Source: Asking many questions of AlgorithmX2 in IRC, not personal experience.)