Hello Bryan,
If I understand you situation correctly, it would work to have the layer just “turn off” for a period of time, and then resume later in the piece.
You are correct there is not a way to set an end point and then later ‘resume’ a layer, since After Effects thinks more like Photoshop (building a layer stack) than a video editor (a sequence of shots across time.)
But the simple solution is to just keyframe the opacity (shortcut T) to change from 100% (or whatever opacity you are using) to 0% in the next frame, and then back from 0 to 100 when you wish to resume the layer.
You can also keyframe the position of the layer while it is invisible to have it “resume” in a different place if that’s what you need.
Hope that helps!
Declan Zimmermann
Design & Motion
motiongraphicsnyc.com
twitter: @MographNYC