Yes, you can make payments from Trust while in your invoice batch by using the batch Trust Payments feature.
Once a batch is created you will see the Trust Payments tab next to your Invoices tab. From here you will see each one of your invoices, Amount Remaining, Trust Account, and Funds Available.
You can choose which Trust Account you would like funds to be deducted from and it will automatically put the Payment Amount in the field for you but you an edit this as needed. You can also change the date of the payment (instead of saving it as of that day) and click the Pay button.
Once payments have been made you can go back to the Accounting for your clients to edit the payments if needed.