If you have either the appropriate One World Status or are prepared to pay then you can select seats anytime you like.

TBH without status or paying it’s unlikely you’d get to sit on the upper deck.

You need to ask AA for the BA booking reference so you can manage your flights using the BA app / website.

5 hours is more than enough to get from T3 to T5. MCT is 90 mins and most people do it in a lot less time than that so you’d have plenty of lounge time.

if you need assistance you should call BA special assistance - details on the BA website.