The sentences number 1 and 3 i.e. "Put it in separation." and "Put it separately." seem to imply the same meaning but i think sentence number 2 "put it apart."has a different meaning. There should be "Put it aside." in order to have the same meaning as sentence number 1 and 3.
As they stand, #2 sounds odd, and #1 and #3 do not even sound acceptable English. Can you give us some more context? what exactly are you trying to say?