Hm, what do you have to do per part?
To be clear, if all your parts are top side, and already use 3D models on Mech 13 (or whatever you're standardized on), set as top side models and aligned relative to the board top: then, you don't have to do anything, they will automatically be placed on the respective layers when imported into the PCB.
You can query objects across the library but it's jankier than for example querying and inspecting objects across SchDocs. In particular, you can only undo on the current part, not others / globally (and it will warn you as such: "the operation cannot be undone"). So, if you do need to edit things this way, save frequently or make copies, and check everything regularly to make sure you're doing the edits you think you are.
Tim