Many programming languages (include LaTeX) have compiler directives–a type of pragma in the form of a specifically formatted comment. For LaTeX, de facto directives have evolved compatible with popular LaTeX editors including Atom and TeXstudio.
Specify LaTeX compiler
At the top of your main/root LaTeX document:
% !TeX TS-program = xelatex
or other compiler of your choice.
Specify root/master LaTeX document
Particularly for large or multi-chapter LaTeX documents, it is good practice to have multiple documents.
To help your LaTeX editor recognize which is the top-level master document, in the other .tex files you
\input, put at the top of each of those .tex files:
% !TEX root = thesis.tex
or whatever your main document filename is.