How do I write the methodology part of a paper if I use commercial software? I research the aerodynamics of an air vehicle. I use commercial fluid-dynamics software (we have a commercial license). However, I noticed that most papers dealing similar research use homemade software and write about it in the methods section of their papers. 

Should I describe how I operate the commercial software in the methods section of my paper? If not, how should I organize this part of my paper? What aspects should I cover in my paper?
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!