Organizing WordPress For Multi-Site

I have really been trying to figure out the best way to organize a wordpress instillation using the root domain, but also allowing for the ability to add other scripts and files within sub-directories (that don’t get controlled by wordpress). Before jumping in, I really need to know the best way to go about this.

For Example:

1. https://www.newsite.com (wordpress site)
2. https://www.newsite.com/subdir1 (not controlled by wordpress and taken over by wordpress URLS) – Note: would like the ability to remove other directories from wordpress control.

What is the most efficient way to go about doing this?

Should I install wordpress in the root directory or in a subdirectory.