All in one folder

This is the option I prefer and set up on my local dev environment.

Localhost http://localhost points to /var/www/ directory, where is located MODX directory and all packages.

• var
  • www
    • modx http://localhost/modx
      • assets
      • core
      • setup
      • ...
    • package1 http://localhost/package1
      • assets
      • core
      • ...
    • package2 http://localhost/package2
      • assets
      • core
      • ...

In this case set Packages directory to /var/www/ and Packages base URL to /.

Separate MODX, separate packages

Localhost http://localhost points to /var/www/ directory, where the MODX directory is located.
All packages are located in /var/www/packages/.

• var
  • www
    • modx http://localhost/modx
      • assets
      • core
      • setup
      • ...
    • packages
      • package1 http://localhost/packages/package1
        • assets
        • core
        • ...
      • package2 http://localhost/packages/package2
        • assets
        • core
        • ...

In this case set Packages directory to /var/www/packages/ and Packages base URL to /packages/.

Packages under MODX

This option I mostly use on remote environments like MODX cloud.

Localhost http://localhost points to /var/www/ directory, where is located MODX.
All packages are located in /var/www/packages/.

• var
  • www http://localhost
    • assets
    • core
    • manager
    • setup
    • packages
      • package1 http://localhost/packages/package1
        • assets
        • core
        • ...
      • package2 http://localhost/packages/package1
        • assets
        • core
        • ...
    • ...

In this case set Packages directory to /var/www/packages/ and Packages base URL to /packages/.