Keep raw geometry [edges/faces] on Layer0.
Always have Layer0 set as the active-layer - never change it.
Select commonly oriented faces [double-click to select their edges to] and Group, or make Component if you will use the same thing repeatedly...
Make a new Layer if a suitable one doesn't already exist.
Now use Entity Info OR the Layer toolbar drop-down and assign the Layer to that Group/Component...
Now these will switch on/off in the Layer Manager dialog and there's no confusion about some faces having edges that on other layers an so on.
Remember that Layers control visibility BUT a Group/Component separates the geometry - think of each Group/Component as a separate mini-model within the main model...