I think I figured it out. For each app (with different layers than the other apps I have), I will need to create new WebMap in AGOL, this will allow me to generate a new AppID.
So, I have 2 WebMaps I created in AGOL. WebMap1 and WebMap2. Each has different layers. Each has a unique AppID.
Next, I would install 2 copies of the Web AppBuilder Developer Edition 2.0 in separate folders on my local drive. Let's say I name each folder, FolderX and FolderY. Each contains a separate install of WAB Dev Edition 2.0.
Each WAB install would reference a different AppID.
If I wanted to add/remove layers from WebMap1, I would do this in AGOL, then I would open the WAB in FolderX to make any further adjustments; if I wanted to add/remove layers from WebMap2, I would do this in AGOL, then I would open the WAB in FolderY to make any further adjustments.
OR
BEFORE I open the WAB Dev Edition 2.0, I would go into the signininfo.json and swap the AppID which references WebMap 1 with WebMap 2, and vice-versa. Is this possible? (this approach means I would not have to install 2 completely separate installations of WAB on my computer)