You can specify after which page to insert a stitch-in. If you have multiple stitch-ins, it can be a good idea to specify the front and back content of the stitch-in so that you can tell them apart. If it is a whole book you're including, it is the front and back cover of the book. If you want to create a flatplan for the book itself, then you can do so on a separate flatplan.
The system does not alert you whether the stitch-in can be inserted after the page you set. You need to do your own manual calculations and ensure they are correct.
You can see the stitch-ins on the flatplan, and if you click the stitch-in you can see the front and back content. Click the line again to clear the pop up.