The easiest way to remove ponding water from a flat roof is to remove high spots instead of filling up low spots. most people will try to fill the lower areas on a roof to prevent water from pooling. The easiest solution is to make a channel or remove the high spots which prevent water from flowing.
Watch more videos on how to get rid of ponding water:
Removing pooling water on a Residential roof – https://www.youtube.com/watch?v=GwwF2WyyGIw&t=11s
Making a channel to remove pooling water – https://www.youtube.com/watch?v=5Gzc9D4UnIY
Channel and strainer made – https://www.youtube.com/watch?v=UjplsNHj7JA
0:00 Explaining water ponding
1:19 Find the lowest section of Pond
4:29 Cutting roof to remove insulation
6:22 Removing screws
7:32 Results after removing insulation