Your EMI will be highly related to your layout, so start with that first and make provisions for filters on input and output side.
If you add parasitics to your schematic, you will be able to simulate low-frequency behavior (say <10 MHz) to a reasonable level and perhaps tune your filtering accordingly. Higher frequency stuff going on, diode ringing and similar, would require very accurate models and the capacitive and inducting coupling between components would make your model a lot more complicated. I've seen software trying to do that for you but I've never seen it done myself.
EMI is a holistic subject and trying to fix everything on schematic level is borderline impossible. If the manufacturer have any application notes on layout and filtering, start there. If you have custom magnetics, you need to be aware that it's a big unknown to them and you need to get to know it by prototyping.
If I where in your shoes:
- Layout, layout, layout. Most EMI problems stem from bad layout.
- Transformer construction. There are many ways to construct a working transformer which will do what you need on DC level but they will have vastly different EMI performance. It takes a lot of know-how to construct a transformer for low EMI.
- CM, DM and general filtering on input and output.