In order to create a 'pending' invoice, the payment method you use for the order must allow you to.
For that you need to add in the payment method's model this member:
protected $_canCapture = true;You can add it right under
protected $_code = 'PAYMENT CODE HERE';For example if you want to do this for Check/money order you need to add the line above in app/code/core/Mage/Payment/Model/Method/Checkmo.php
After this when you create an invoice you will have an option near the save button to set the invoice status. (see picture attached). To create a pending invoice select 'Not capture'.
If you want to mark it later as paid edit the invoice and between the buttons on to one called 'Capture' (see picture). Well you get the idea....