I have tried adding a line item but it adds that $12.50 to the total.
I have also tried a custom field but it is manual and there is the potential for user error (as always). I would like something to automatically calculate this and print it on the invoice for me.
A deposit due should not appear on a sales invoice for the reason that it should already have been paid to you by the time you issue the sales invoice. Notice that a required deposit should be a condition of the contract, expressed as a note in a custom field on a sales quote. The sales quote could also be issued as a pro forma invoice. See Create sales quotes | Manager.
Acceptance of the deposit should be recorded on a receipt, posted to the customer’s subaccount under Accounts receivable, as explained in this Guide: Record customer deposits and advances | Manager. To avoid mistakes, the receipt could be copied from the sales quote mentioned above.
When the sales invoice is ultimately issued, the deposit will be automatically deducted from the balance due, as also explained in the second Guide linked above.
Manager will not automatically calculate amounts. But it will allow you to enter calculations into the unit price field. See the Guide about calculations: Perform calculations in number fields | Manager.
@Tropilac, the capability @Ealfardan refers to is introduced in this Guide: https://www.manager.io/guides/17115. That Guide is not, however, a complete tutorial. I should have been more explicit in my earlier response. Manager will not do what you want on its own, meaning there is no built-in option or control. But you can create a custom theme that will perform that function if you have or can hire the necessary programming talent.