These are things you need to figure out. Don't make the mistake of thinking that you can design concrete however you want and make it work. Concrete is how it is, and you have to analyze it in a way that approximates reality.
An example would be saying there are two simple span beams on either side of a column. The reality is that there is a continuous beam, and the maximum moment will occur over that column. It will only act as a simple span beam when significant cracking occurs on either side of the column (right where the shear is at a maximum).
How much moment transfers into a column from a continous beam is a function of the stiffness of the column versus the beams. If it is a negligible amount, you could treat the column as a pinned support.
If I was you, I'd figure the moments in beams and columns out on paper as well as I could, and ONLY THEN put the members into a software program such as RISA 3D or SAP and analyze it. Make sure you figure out exactly why you made your mistakes. Your boss probably wants an answer "quick", but if you just rely on software, without fully understanding, you'll be giving him a solution you aren't sure is right, and next time you have a similar problem, you still won't understand it.