I totally agree with you Stacy.The dogs will decide who will be top dog and it sounds to me it has already been decided
As long as Cooper is happy with her being boss and doesn't have a go at her I think you should treat Haley as top dog.
I was in the exact situation when I got Melody,it upset me at first but it doesn't bother Charley.Male dogs usually arn't bothered they will normally step aside (like men do

) The girl dog normally ends up top dog from what I have heard.
Treating Cooper as top dog could make things alot worse.
Just make sure you still spend time with him such as maybe walking them seperate sometimes,or go into another room in your house and spend some playtime with Cooper.
Also I wouldn't leave them alone with toys or chews,make sure you are always there to supervise them
Sharon,Charley & Melody xxx