Yes, once you release the customer order, if the charge is not connected to a line, it should be ready to be invoiced.  You can see this via Quick Order Flow Handling. 

The key to the process is to print (which in turn posts the invoice), prior to creating the invoice for the customer order line. 

If you do not print the charge invoice, when you create the invoice for the customer order line; the IFS Application will automatically add the co line to the charge invoice.  Does this make sense? .