So,
Ref; Default layer zero;
It's a greedy DEFAULT layer that you cannot delete ... zero cannot delete anything, or move its contents into your current layer.
Solution; -
Keep the 'entity info' window where you can see her. (Always! ... not unlike 'properties' in AutoCAD)
Ditto layers window. Again, always there.
So:
Go to your model; define components by select-dragging top left to bottom right over just one component.
Go to your newly opened 'entity-info' window and click on the drop-down arrow, by layer, and choose the (appropriate) layer, (Not Zero,) With each. If in doubt - go to Layers and type in an 'add' to make a descriptive layer. You'll see what we mean when you get there.
But just in case it's even more complicated ... maybe you have inherent components that are not entirely sure which layer they belong;
If you don't mind exploding and re-componenting (although expensive on file size,) the ultimate fail-safe is to have absolutely everything in the layer you want; if its got confused; 'explode' and re-layer.
Anyway, ref your question; Is there logic re secondary layer ... yes.