What "lingtrin" said is correct. You will have to change the qty to invoice field to the right amt of qty you want to invoice. Qty is allocated only for Sales Orders and invoices and not for quotes.
1) Create a Sales Quote
2) Once the order is confirmed from your customer, transfer the quote to Sales Order or Fulfiment ORder
3) in the Sales Order, leave the "Qty Ordered" field as it is. Expand the line and edit the "Qty to invoice" field - set the value to the qty that you are shipping/invoicing your customer for
4) transfer the order to invoice. This will transfer only the items that have Qty to invoice value set, and only for the qty being invoiced - not the entire qty on order
5) Post the invoice and the inventory is sold
6) When ready to ship next batch, go back to the Sales Order, and edit the Qty to invoice and transfer the order to invoice and follow the process of posting the invoice to confirm the quantity sold
When in order, the quantity is already allocated even after transferring the partial order to invoice. For Ex, for item 128 SDRAM, qty order = 30, qty to invoice = 12. balance on order = 18.
For the order, the qty allocated = 18 and for the invoice the qty allocated = 12. So your quantity of 30 total is still allocated. When posting the invoice, the Allocated changes to 18 (based on order) and the Sold qty increases by 12 (the invoice that was posted)
You could use SOP Orders or Fulfilment ORders for this