Modeling floors with with two different elevation supported by same girder

RAM Steel does not design a split level conditions to this level of precision. If you want to model everything as flat, on the same level, then the girder can certainly be designed for loads from both sides. The fact that one beam is supported by the bottom flange might require you to do some hand checks for the girder flange locally, but the overall flexural design should be fine.  

If you decide to model this using 2 stories, then you'll need a double beam, one on each story, to simulate your deep girder. I've seen some users model the lower level beam as a long transfer beam and then model a series of stub columns going up from there to pick up the framing of the higher story, but this seems like a lot of work for little gain.