When you do a new install of D365 it will have been done through LCS. So you would have created a project to manage the deploy you could use that or another project to manage the implementation documents and procedures. So after you have deployed then you should go into the system administration to change the help settings to select the project you want to work with.
This is important if you later want to deploy artifacts from LCS for example PowerBI or update task recordings to the BPM library.
Here is a quick overview.