In the assembly model you can select the option in the properites tab to not include these items in your BOM. This should help you.
As Michael said, in the assembly you can right click on the component name in the tree, choose the Component Properties icon, and click "Exclude from BOM" in the lower right corner of the dialog box. Or, you can drag the row to the bottom of your BOM before hiding and then you won't have a skipped number.
Thank you both for the reply. I have taken the Solidworks University provided by our vendor and I know its hard for them to touch base on everything. Learned something new today!