Umar is right. Use section modifiers for serviceability checks.
This set of modifiers are mentioned in section 10.11.1 of 05 addition which is dedicated to computation of lateral deflections of frame. Remember that code specifications are based on worst case scenario, and these values are worst case scenario for lateral deflections of frame.For elastic analysis of frame it is OK to use gross properties based on rectangular section as it is done in ETABS . We provide rectangular beam section properties in ETABS, but cast in place beam has T section in positive region while rectangular section in negative region, so using rectangular section along entire length compensates for that.
Moreover if bottom reinforcement of beam is developed in column, as it is normally done, it increases stiffness of beam in negative region. Amount of reinforcement provided in section also plays its role and we dont know how much reinforcement will be required before starting analysis.
Bottom line: it is complex topic and one have to use assumptions. Even if one is using 0.35 and 0.7 factors to size the xsection of member, structure should still stand provided assumptions are uniform through out the analysis, as concrete has this ability to distribute moments according to provided reinforcement.