Invoicing part orders that have a full payment allocated

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Hi All,

We receive orders through our website, and the sales orders are entered and the payment recorded under the tick box "Record Payment with order" 

However, this has caused issues because we part despatch orders, and you cannot generate part invoices if you have recorded the payment as above. 

What is the best way to record the payment on the sales order, but also allow us to part invoice? As we could be waiting a few months to invoice the order as full - which in terms of profit tracking for the month is not suitable for us.

Thank you!