How am I supposed to design larger projects in c++?

I am trying to create my first significant project and learn the fundamentals of graphics. As part of this endeavor, I am developing a software renderer and attempting to implement most of its components from scratch. Since this is a larger project, I am uncertain about how to design things, and it's a little confusing for me at the moment. Currently, I am trying to have a single instance of the engine that other classes can use as a sort of bridge to the core parts of the program. I have read everywhere that singletons are considered bad practice, but it seems to be the only way I can wrap my head around how to structure a program like this. If anyone could point me in the right direction, I would appreciate it.

here is the repo: https://github.com/LeeMclafferty/SoftwareRenderer