can i record a deposit received to an open sales order?

Not specifically but there are a few ways you can handle it .....

• Receive the payment as normal under the Customer/Customer Job & it will reflect as a Credit until you convert the SO to an Inv, at which point you then apply the payment to it
• Setup 2 Deposit Items - 1 for upfront received as an "Other Charge" type & 1 for allocation as a "Discount" type, both linked to a newly-created Liability account (eg "Deposits Held")   Record the Deposit (received upfront) via a Sales Receipt then minus the Deposit line off (using the allocation discount) on the subsequent Inv

The first option is far simpler but if multiple deposits are frequently held &/or for extended periods of time, the second option allows for tracking & reporting of this in more detail. 

The 1st (Sales Receipt) transaction puts the deposit into the liability account but the 2nd (Tax Invoice) transaction is also required in order to clear it out again!   How has the final sale been being recorded & the deposit on it been being reflected ?  Where to go from here, depends what's been happening/reported so far.  

Note: Usually, there's no GST on Deposits so no tax codes are used on these transactions.  However, be aware that if you've only been invoicing remaining balances, you've been under reporting both sales income & its GST 😫  

Firstly, I'd recommend generating a report on your Deposit Received account & identifying which (if any) Deposits are still actually being held currently.