In my experience, sub up port back only gained from about 45-55hz. It was louder in that range but the low end was terrible. It made things really peaky.
This is what I have typed in another thread almost identical to this one:
I really wouldn't do subs and port up in a '99 integra hatch. You lose a ton of low end doing that. I would do sub and port back as close to the rear as possible. That's how I run subs in my '99 hatch and I have experimented with these different configurations:
sub and port facing me
sub and port facing rear
sub up port up
sub side port side
sub up port back
sub back port side
In all those, I will take sub back port back any day of the week. If you only care about being loud around 45-50hz, sub up port back works well but there is nothing below 40hz for me. Sub back port back has a nice response dropping pretty low with the hatch resonating around 30hz so it added a nice gain. I only really got this with sub and port back. When I put some expanding foam in there, this point went up to about 38hz.
Another thing... I owned an IDQv2 12d2 and it definitely had the flattest response and the best sound with sub and port facing the rear. Oh, and rattling isn't a huge problem with those cars. They flex before they rattle and they flex all over.