Option #1: Create a Promotion called "Manual Cash Discount" using the Cash Discount Calculator (The Cash Discount Percent on the Setup POS & POS Devices, that is a rounded number and will likely result in often having penny errors) for Services & Products and manually apply it to the Services & Products only.  

Note: This method still can result in being short by a penny because of the fraction calculations. 

Option #2: Create a payment type called "Manual Cash Discount", then apply a partial payment for the difference between the Non Cash Total and Cash Total.  For example if your Non Cash Total was $103.75 and your Cash Total was $100.00, the Manual Cash Discount Payment would be $3.75. Note: This would not work on automated Memberships. 

Consider your setup for Process Compensation - if you're paying commission on the Paid Price, the calculation would only pay on $96.39 but if you're paying commission on Set Price, it will honor the full $100.00 service price.