How do I indicate where Emscripten should locate source files during compile?

I'm sure this question will need editing, yet, being mostly a Javascript programmer, I'm really not quite sure how to phrase it properly. My problem is locating source files during compilation with Emscripten. My "include"-commands refer to source code, such as "Core/main.h", which in turn refers to other source files in the same folder, yet using a similar address, (e.g. "Core/app.h")

How do I overcome these "File not found" errors? How do I indicate to the Emscripten compiler that it should look in the source folder? I've been reading the documentation, but it what I'm finding discusses, I think, virtual file systems for use during run time, not included directories during compilation.

I know this question is a mess. Sorry, still getting the hang of compiling C++.