Last time I looked, Luban was not able to handle multi-pass milling jobs with tool changes. Admittedly, this is a while ago, but what you describe sounds very much like nothing has changed. That said, you’ll need another piece of software to generate the toolpathes, many people use Fusion 360. Fusion 360 does “Rest machining”, i.e. if desired understands that the previous tool removed a lot of material that does not need to be removed again.
@Skreelink put together a very extensive guide that should help you a lot: Fusion 360 Guide For Multi-Pass 3D Engrave