How do I write the methodology part of a paper if I use commercial software?
Since my background is also CFD, maybe I can help.
It is really important to mention what type of scheme you are using and what is the commercial software. Is it based on the finite volume method or finite element method? Is it a cell-centered or vertex-centered scheme? What is the order of convergence of the method you are using, are they first, second or third order in space? Which transient time-stepping scheme are you using? What is the order of convergence of that scheme? Is it implicit, explicit? Etc.

In the end, the commercial software is just the implementation of a numerical scheme that you are using to solve the Navier-Stokes equation. It is important that you highlight the equations you are solving, the type of turbulence modeling you might be using and also the properties and details of the underlying numerical scheme. Then, even if you are using a commercial software package, people will have sufficient details to understand the context of your numerical resolution.

Also, please do not forget to carry out grid-independence studies!