How to stucutre my website and configure my .htaccess

I am really just now getting into web programming, I do know Powershell, C++, and C# but I am just wondering a few things as I dive in.

Whats the best way to structure the folder? Do you put different portions of the site in different folders? Like Logins in one, profiles and users in another etc? Or do people generally leave everything in one big folder?

In my .htaccess file what would my file look like based on a good folder structure? I tried everything flat, then the server guy came out and I threw everything into folder like logins, register, profiles, with the html and php files for that portion under the directory. Im having a hard time understanding how to write a htaccess file to only show the folder, and mask the file and name. I also have a file share in there. How would you rewrite the URLS to generate a random download link. Is that even the right wording? Hell I dont know.. Any help would be greatly appreciated!