For the engraved areas, you will likely want to make sure that the paths are closed for each section. It’s not going to matter for any scoring - just make sure your colors are consistent. But you can get some unexpected results trying to engrave open paths.
Are you using Snapmarks for aligning? If so, there’s a writeup here on how to use them for Passthrough work…you can probably use them the same way for separate sections.
Or if you don’t have those yet, you can try indexing marks: