How do you over lap two notes without useing the "Layer With Next Staff" feature??
Insert the first note with Enter, then move where the second one should be and enter it with Ctrl+Enter.
If both notes are at the same horizontal position, you'll have to enter one with its stem upward (Shift+Up Arrow) and the other with the stem downward (Shift+Down Arrow).
With this technique, though, the possibilities are more limited than with layering. I let you read the help file for more info.
I hope this helps.