https://teanmoon.blogspot.com/2019/01/whats-in-clone-guide-to-cloning-meshes.html

In the warehouse tab you can see all the cut layers for all the lods listed as geometry. This mesh has 4 LODs and 3 cut layers per LOD, so there are 12 geometry entries.

The third geometry entry shows the chunk missing from the dress mesh above.

If the arms do not have the correct cut number they can end up inside the body like in with the dress above. I have also seen them hanging off sideways in this scenario.

If the knees and ankles do not have the correct cut numbers, putting on boots can cause pieces of your mesh to disappear, like the body of the dress did here.

The region map can be found under the warehouse tab. To edit the region map you need to click the Edit Items button under Entries.

This is the typical region map set up for a pair of pants that tucks into boots.

Here's the typical set up of the region map for a pair of tall boots. You can see that the values for Calf and Knee are both higher than corresponding values on the pants. The boots are a higher layer number than the pants, so the pants tuck into the boots.