SubPages Extended comes with a really handy shortcode functionality. Using its shortcode [subpages] you can change output of the plugin in many ways. Here are a few common usage examples for the shortcode.

SubPages Menu Depth

[subpages depth="2"] – show the list with a depth of 2

Excluding Pages from SubPages

[subpages exclude="2,4,12"] – exclude subpages with indexes 2,4 and 12

[subpages exclude="4" depth="0"] – exclude post id 4 and show all subpages.
[subpages depth="1" childof="257"] – show subpages of page with the Id of 257
[subpages depth="1" childof="257" exceptme="true"] – add current page to the exclusions. This way you can show links to other subpages of parent easily. See the bottom of this post for a demonstration.