At the moment ReadyToShip doesn't allow splitting of one order into separate orders, or partial fulfilment of single orders.
If you want to you can process orders like this manually in your carrier (outside of ReadyToShip), or alternatively you can split orders in your webstore/marketplace account. Then ReadyToShip will import separate orders and all should be fine.
We are working on adding this functionality in ReadyToShip and when it is available in 2018 you will be able to split orders, partially fulfil, or manually add orders.
If you process orders outside of ReadyToShip, sometimes orders in our system may turn red to alert you that changes have been made. Click here to see how to deal with that.