The best EMI filter is the one that you don't need. So you'd typically start by running the circuit in SPICE, and add parasitic properties of key elements. E.g. decoupling capacitors have ESR and ESL (equivalent series resistance and inductance, respectively). That way, the AC current flowing from the power source is more realistic. And so you know exactly what frequencies are there. Next, your goal is to make those AC currents flow inside your circuit and not reach the power supply, the outputs, the external connections, etc. The first step will be to arrange circuit impedances such that most of the AC current flows in small loops. Some of it will inevitably escape due to nonidealities of components and layout, and that's the part that the EMI filter would deal with.
The approximate process would be as below, and some groups of steps have to be iteratively repeated.
Design the basic circuit and get it to work in SPICE at least.
Choose actual components (real part numbers).
Use the component data sheets and/or characterize the components using a network analyzer to obtain their accurate simulation models that include parasitics.
Substitute equivalent networks of real, non-ideal components for the ideal components in the SPICE model.
Identify the AC current loops of concern in the SPICE model.
Lay out the circuit taking critical current loops into account.
Use an electromagnetic simulator - this could be your head, with enough experience - to approximate the parasitics of the layout.
Add the layout parasitics to the SPICE model.
Re-run the simulation and observe the AC currents flowing from the power source, flowing to the output, flowing to the I/O ports, etc.
Do various things to constrain those currents to flow within your circuit only. The EMI filter is the last line of defense that will do that.
Notice how we haven't actually put anything physically together yet. If your simulations are accurate, as soon as you assemble the prototype, it should work and pass EMC testing at least in respect to conducted emissions - since you were simulating all that.
The simulation model may have some infidelities, which you would now identify by comparing the performance of the prototype with that of the model, and adjust the model to more accurately represent the real circuit. Then the simulation will inform you what changes (if any) are needed to the EMI filter to get things to pass.
It is generally a tall order to use external filters to work around deficiencies of a badly designed circuit. And, unfortunately, the majority of little "switching converter" boards sold for the hobby market are quite atrocious in terms of EMC - precisely because nobody tried to make them behave just by themselves, without external filters. This is a real problem in low-level circuits that are noise-sensitive: with a few "handy" buck/boost/charger boards on the breadboard, you get an intractable mess that takes real effort to clean up in terms of EMC needed just to get it functional - that's even before you begin to think about any other EMC testing.
Some people would argue, and rightly so, that EMC is part of the functionality of the circuit. Thus there's no "make it work" separate from "make it pass EMC testing": it's all part of the same process, and the first prototype should at least have first-order effects taken care of with EMC in mind.