How does Midas Civil distinguish between short-term and long-term load and apply the modular ratio accordingly? Does Midas take Creep into account for any loadcase we include in the construction stage?

Construction stage analysis is generally used where time-dependent properties (compressive strength gain, creep and shrinkage) are defined. Based on time-dependent properties, the effects of long-term loads are observed.  

Post CS stage (after the construction stage), concrete would have gained strength and short-term loads are applied generally after construction stages as the modular ratio is observed accordingly. 

But if construction stage analysis is not performed, short-term and long-term modular ratios can be defined while defining the composite section property, as shown below.

Note: These modular ratios are overridden if construction stage analysis is performed.