I don't know about resetting your existing object layers settings, but, I do know what you can do to avoid this in the future. Open up your template file. In your prospector window, right click on your drawing in the list, edit drawing properties. In the object layer tab of the new window, set your civil 3d stuff to specific layers.
In my template, we also use wildcards in the layering, so an alignment, chose a layer called "Align-" and give it a wildcard mark at the end. If your alignment created is called Street A, then when the alignment is created, the Civil 3d alignment will go on a layer called "Align-Street A", or "Align-Street B" if you called it Street B, ect... There are various ways to go about setting up the Civil 3d layering stuff- wild cards prefix, wild card suffix, no wild cards, ect...
I guess you could set this in your current drawing and also change the C3d entities to the new layers, but that will probably take awhile if you've gone a long way in your file.
Hope this helps.