I want to ship partial orders. As user has order some product which is currently not available in stack how can I achieve this ??
You can achieve this by adding product qty which you want to ship. Magento provides partial shipment
Shipments With Magento Inventory Management enabled, you can send partial or complete shipments from one or more sources to fulfill orders. You control your outgoing inventory for each order, setting the amounts to deduct, sending one or more shipments, and delivering in stock and backorders as inventory is available. For each line item in the order, enter an amount to deduct from the source quantity. Generate a shipment per source as you have inventory stock, until the entire order is fulfilled.