Check if this suggestion works for you:

I will use this example:  Your Customer purchases $500 worth of Services, but sells you $300 worth of Products, so you want to offset the $300 you owe them against the $500 you owe them and just pay them $200.

One way to do this is to setup two additional accounts - AP with NETTING and AR with NETTING.  You then assign the AR and AP accounts of Partners who you have a netting agreement with to the same account. Do this based on what that Partner does MOST of the time.  If most of the time they BUY from you - their AR and AP accounts would both be set to AR with NETTING.  If most of the time they SELL to you, their AR and AP accounts would both be set to AP with NETTING.

You have to get around the business rules that prevent you from choosing a Payable account for AR and a Receivable account for AP.  You do this by importing the new Accounts instead of changing them via the User Interface.

1. Create the two additional Accounts. 

Via Accounting --> Configuration --> Chart of Accounts:

2. Filter for the Customers and Vendors who you have netting agreements with.

Export their NAME, ACCOUNT PAYABLE and ACCOUNT RECEIVABLE. Be sure to use the EXPORT ALL DATA option so you can export the Accounts by their name:

You will end up with a Text File that looks something like this:

"External ID","Name","Account Payable/Name","Account Receivable/Name"
"__export__.res_partner_7","Customer","Account Payable","Account Receivable"
"__export__.res_partner_8","Vendor","Account Payable","Account Receivable"

Edit the account names, to match the ones you made in the first step:

"External ID","Name","Account Payable/Name","Account Receivable/Name"
"__export__.res_partner_7","Customer","Account Receivable with NETTING","Account Receivable with NETTING"
"__export__.res_partner_8","Vendor","Account Payable with NETTING","Account Payable with NETTING"

3. Import the file to change the accounts.

Be sure to map the fields properly for the Accounts:

4. Create Customer Invoices and Vendor Bills as you normally would.

Review the Partner Ledger and Aged Receivables Reports to verify how the 'balance' for the Customer has been computed:

In this case I created a Customer Invoice for $500 and a Vendor Bill (from that Customer) for $300. 

You can see from the Aging Report above that we owe the Customer just $200.

5. Use the Vendor Bill to 'pay down' the Customer Invoice. 

Open the Customer Invoice - you will see the blue notification and the 'payment' you can apply:

Apply the 'payment' to reduce the balance of the Customer Invoice.

The Invoice and Bill will now have the following balances - Invoice $200 - Bill $0.

Review the Aged Receivables report:

Be sure to review the Ledger treatment of these transactions to make sure they satisfy your local Accounting laws.

Note - the choice of whether a Partner is "mostly a Customer" or "mostly a Vendor" determines which Report they show up on.