Sprite Editor (?)

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Hi there, although not new here, my coding is.
I have created a grid and now want to populate it with tiles or sprites or whatever.
First I want the background - each cell can have a different one, then I will want to create items to overlay, eg, castle, infanty, whatever.
So I know I will need 2 or 3 layers.
BUT... how do I go about making an editor to create the actual tile ?
How can I make the background see through so that I dont overwrite information ?

Oh, and my grid...its a hex grid.

Any pointers REALLY appreciated.
CJS