I find that the best way is to store the entire ~/.emacs.d directory (including the /elpa subdirectory) in a git repository. This makes it easy to keep your entire config in sync between machines, and it means you keep your init file in sync with the versions of packages. Otherwise you may find that when you install your init file on a new machine and install the same packages, you get newer versions that have breaking changes, and it usually happens when you don't have time to fix it.
If for some reason you don't want to do that, the use-package macro makes it easy to install packages, like: (use-package org :ensure t) That will install org using the package system, if it's not already installed.
