Glad that helped!
You can see a video on using the Secondary Nav here: https://generatepress.com/downloads/generate-secondary-nav/
What kind of custom links? Just regular links in the widget?
If so, you can use a Text widget and add this HTML:
<a href="http://generatepress.com">GeneratePress</a>
<a href="http://google.com">Google</a>
<a href="http://wordpress.org">WordPress</a>
And so on.
Then check the “Automatically add paragraphs” checkbox and you’re good to go 🙂