Sorry, not full understand yours problem.
When you try show some module ( e.g. new books ) for Book library software - you need chose for it some module position.
You may show modules in Joomla only in module positions.
You may add module to some article show with help:
You need put above row to article text - and yours articles will show module.
Or you need put some like above row - to yours template - and with that - you will can see book module (and any other) in any yours joomla site position