If you have files that you want to integrate into the MiKTeX setup, you have several options:
Use the command-line option
latex --include-directory=C:\path\to\my\style\files thesis.tex
See the section called “Specifying Additional Input Directories”, for more information.
Set environment variables
set TEXINPUTS=C:\path\to\my\style\files latex thesis.tex
See Chapter 8, Environment variables, to learn more about MiKTeX environment variables.
Register a user-managed TEXMF root directory
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.