Standing water on the roof surface should be eliminated, or it will bring nothing but trouble. The development of low spots that collect water is an indication that there is not enough structural support for the type of roof decking that was used. Because you have a good rubberized membrane on top, you will want to tackle the problem from the bottom. Open up the ceiling below and add cross bracing to the structure to level out the roof deck. If you decide to do this, start with one small hole in the ceiling below the worst depression. Inspect the roof deck to see that it is not simply sagging or rotten. If it is rotten, you cannot tackle the problem from below. If it is sound, then proceed. If you have to rebuild the entire roof, use good materials and be sure that the new roof is built high enough above the walls to permit good insulation and good ventilation.