Should all C++ code in a project be encapsulated into a single class with main simply calling that class? Or should the main function declare variables and classes.
If you are going to build a large project in C++, you should at the very least read Large Scale C++ Software Design by John Lakos about it. It's a little old but it sounds like you could benefit from the fundamentals in it.
Keep in mind that building a large scale system in any language is a challenge and requires skill and discipline to prevent it falling to pieces very quickly. Don't take it lightly.
That said, if your definition of "large" is different than mine then I may have alternative advice to give you. I'm assuming you're talking about a project where the word "million" will be mentioned in sentences that also contain the words "lines of code".