Access to other custom php pages
The default path or root directory of any Drupal site is the same directory/folder which contains the site itself. ie. Same directory which houses the "sites" directory. If I put a php file there called "my_code.php", any reference to the file will be seen by everything as default. Its when other directories are created and the file placed there which make a file's location more specfic. So if I'm in a php file in another directory and I put in a statement like:

include 'my_code.php';

Drupal will start by looking in its default root directory. If I create a directory there called "my_php_files" and put the "my_code.php" file inside, then my reference to include that file would be:

include 'my_php_files/my_code.php';

Default permissions are normally 755 for directories and 644 for files.