Fixing the slope of a flat roof
I see two solutions: 1) add slope to your roof, and/or 2) install a tank liner roofing 

1) Adding slope can be done two ways: a) cut tapered wood members and install new roof sheathing and a new roof. This can be done on top of the existing roof sheathing or remove the existing sheathing and sister in sloped joists. Either way it will be difficult. b) install tapered insulation on top of the existing sheathing. Then install a low slope roofing. You can buy rigid board insulation that starts at 0” height and increases 1/4” per foot. It can slope one way or two ways (with a ridge or hip).

Either alternative has consequences. You’ll be increasing the slope so the roof will get higher and could encroach on the upper roof. 

2) Tank liner roofing is basically used to hold water. So, the ponding water you’re experiencing is not a problem. However, tank liners are not made to resist ultra violet rays from the sun so it will decompose in a few years if not protected. I’d install a painted roof coating that reflects the suns rays. You’ll need to reinstall every few years due to wear.