If you have files that you want to integrate into the MiKTeX setup, you have several options:

Use the command-line option --include-directory=dir

For example:

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

For example:

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 directory (usually C:\Program Files\MiKTeX 2.9).

	Tip
	This is the recommended method. You can register TEXMF root directories with the help of MiKTeX Console.