Once you open vim-fugitive's git summary window, you'll see a listing of the tracked files with unstaged changes. Each of those files is made up of one or more hunks—a semi-contiguous chunk of changes in a Git diff.
You can jump forward and backward through these hunks with ]c and [c,
respectively. If the inline diff view of a given file has not already been
expanding, these navigational keybindings will auto-expand it.
With the cursor over the heading of a particular hunk, you can hit s
(assuming you're looking at unstaged changes) to stage the entire hunk.
Similarly, if the cursor is over the hunk heading of a change in the staged
area, you can hit u to unstage that entire hunk.
For more details and a visual walkthrough, check out this screencast on staging commits within Vim.