Layers are a useful way of organising your drawing objects and layers.
Toolpaths however are not controlled by layers.
If your toolpaths are getting a bit cluttered, a useful method is to:
Select the drawing object (this is the very first object at the top of the drawing tree on the left).
Look in the properties grid and the very last property should be:
ToolpathVisibility. Change this to SelectedOnly.
Now CamBam will only display the toolpaths for machining operations you have selected in the drawing tree. If you select the Part object, the toolpaths for all operations in the part are displayed.
I prefer this method and have this set in my default drawing template so all new drawings behave like this.
I hope this helps.