You need to be more specific about what you want to do? From the outset, it sounds like what you are doing is correct and that after creating the mirrored part (don't need to be in an assembly but rather initiate it from the original part) you add additional features to the mirrored part that are unique from the original; this is how it was designed in that when you create the mirrored part, you are deriving all the features from the original part and then adding "on-top-of" them your new unique features. That is why you only have one stock feature in your mirrored part to begin with so it can be associative with the original and the original (base part) "drives" the derived (mirrored) part.
If you desire NOT to have an associativity to the original part (not recommended) then you can break that associativity by RMB on the stock feature in the mirrored part and going to "List external references" and click on "Break ALL" and also optionally you can (before you Break All) you can choose to put all the original features back into the mirrored part.
Thanks for the reply. I decided to redraw the part as needed, as this seems like the best option for future use, as I want all the design tree features.