adding two G+2 retails buildings to the designed building

It still sounds like an NC project. LEED Retail kicks in later this year. You could submit a single LEED submission which includes all three buildings or submit each separately. The window to wall area should be for each whole building. If they are separte then this requirement applies to each building individually. If they are in one building then it should be one model. If separate buildings you have a choice of modeling them separately or all together in one model. If separatley add the three modeling results together to determine the overall percent savings. Not sure why 90.1 does not apply? It applies to office, retail and residential over 3 stories.