I am trying to set up outsourced manufacturing BOMs but cannot include quantities greater than one in the other charge line. Has anyone found a work around for this?

This is by design. Your tolling charge item should be the full amount of the cost so that when you create a PO, the quantity translates to the quantity on the work order or vice cersa.

Create an ‘Other Charge For Resale’ item and replace it on the BOM Revision. You will be able to adjust the BOM qty with that different subtype.