Stock adjustment issues

We issue sales invoices based upon percentages of a quotation, so stock, which has been purchased using PO's is not affected. How do I affect the stock?

If I use the adjustment window, then this should either affect an income or an expense account, which would mean I am double accounting for either inome or expense, as we have purchased the goods, and also sold them, but the invoice just doesn't detail all of the items (it would be far too long and complex for lare projects).

I am sure that there must be a simple solution, however no-one seems to be able to offer one!