If you have files that you want to integrate into the MiKTeX setup, you have several options:
latex --include-directory=C:\path\to\my\style\files thesis.tex
See the section called “Specifying Additional Input Directories”, for more information.
set TEXINPUTS=C:\path\to\my\style\files latex thesis.tex
See Chapter 8, Environment variables, to learn more about MiKTeX environment variables.
Register the root of the directory tree which contains your
files. The directory tree must conform to the TDS standard, i.e.,
you must imitate the directory tree in the MiKTeX installation
C:\Program Files\MiKTeX 2.9).
This is the recommended method. You can register TEXMF root directories with the help of MiKTeX Console.