You can record a new payment against a sales order when your customer makes a payment. This is useful for record keeping it does not link in to any point of sale system).
1. Open a sales order (or save the sales order if already open). Click the Payments icon
2. Click the New Payment button (on the right)
3. Complete the details as required below:
Date Received
Will default to the current date. Change if necessary.
Payment Method
Select from the drop down box e.g. cash, credit card etc.
Payment Type
Select from the drop down box your payment stages (e.g. deposit, payment 1) which then completes the amount.
Click 
Edit Popup Contents where you can rename the default stages.
Amount
Select from the drop down box. The amounts will be shown depending on how you setup payment stages. Otherwise you can click Other and type any amount.
Date Banked
Already completed with the current date but you can edit if needed.
Date Cleared
You can return to the screen to enter the date the payment cleared.
Received to Date and Balance Due
The amounts will be automatically calculated.
4. Click 
Update to save and close the window.
You will be returned to the main payments window where the balance will immediately update.
The new payment will be stored on the Payments tab of the projects screen from where it can also be opened.