start with a simple lid, a cylindrical split line on the inside of your box
use an external inlet or outlet fan
that is a pretty good approximation
from there, i'd do an external analysis and an internal fan
that way you can see whats happening on the inside and outside
then you can start getting closer to reality with perf plates or fan covers...etc. but I wouldn't start there
Jared gives some good advice. I assume that the components and the layout inside your model (which do not exist yet, according to the screenshots) is what is really going to be interesting to you, so maybe don't focus so much on detailing every swirl and vortex that comes from your fan. Just pick a fan and use the manufacturer supplied fan curve, for starters.
The Flow Sim tutorial package has an excellent chapter covering small electronics enclosures, I recommend working through it (if you haven't yet) to get a feel for how the software will handle your design challenge.
I've already gone through the tutorial but I couldn't find an example with a fan inside an enclosure.
So, if I understand well, you are telling me than in this case I can model that fan as an external inlet fan. Is that correct?
That will work, but just keep in mind that it will not take into account any perforated sheet you might want to cover it with in the future. To keep things simple you could model a section of the case as a separate body and model a circular cylinder for the fan. Use the inward face of the cylinder as your "external inlet fan" for now, and in the future you can adjust your model to include an internal fan and a perforated plate without having to adjust your geometry.