When you are recoloring, there should be a little icon, I think it looks like a star or snowflake. If you click on it you will get a drop down box with the different symbols for the different expansions and stuff packs. Match the symbols up and you know which one the item comes from. There is also a filter where you can choose to have only store items showing. It won't tell you which set the item comes from but at least you would know which is store and which is EP/SP.