The link below was a lad who had the opposite problem you do, he only wanted the assemblies.
So if you set your BOM structure to all levels, then all parts and subs will show in your part list.
You will need to delete all existing part lists and balloons in a drawing to allow you to select the all levels part list.
As for quantities, put the same quantities of parts and assemblies in the model as you would in reality, then there are no overrides and nothing hidden, I hate overrides as there is nothing to indicate their presence until you edit a part list or balloon.
Not sure about the underline in the part list/ BOM but you may be able to apply a style to do it and if it did work it would probably be in every cell, although as it has been mentioned elsewhere in this post, I have my doubts.
http://discussion.autodesk.com/forums/thread.jspa?messageID=6269744ꬰ