The main focus of Netshine Billing is on automatically generating invoices based on orders - either orders placed using an order form via your website front end, or recurring invoices for subscriptions. It wasn't really built with this type of usage in mind (ie. building up an invoice for a product based on a number of constituent parts).
Manual invoice creation is meant really for the odd times that you need to create a one-off invoice - it does not look up the SKU or anything. It sounds like you are not using manual invoice creation for the odd one-off invoice, but on a regular basis - so I'm afraid I don't think this is ideally suited to your type of business.
