I have signed up for AutoPay using bank account. Will I still get autopay discount of $5 per line, if I make one-time payment of part of my bill using a credit card, when bill comes

It is super important to understand different discounts because no one wants to miss out on any kind of savings. Pagar AutoPay on T-Mobile Support to get more details. 

• Tener un plan Go5G, Magenta, T-Mobile Essentials, ONE Plan u otro plan con impuestos incluidos (como por ejemplo, LineLink e Internet Móvil para hotspots).
• Tener AutoPay activo al momento del procesamiento de la factura.
• Haber pagado la factura del mes anterior antes de su fecha de vencimiento.
• Las tarjetas con estados de cuenta enviados por correspondencia a una dirección extranjera no pueden usarse para AutoPago.
• El método de pago debe ser una tarjeta de débito o cuenta bancaria asociada. Tarjetas de crédito y billeteras digitales (Apply Pay/Google Pay) no son elegibles.

The last bullet point there means that the payment method on the Autopay has to be one of the eligible types. You can make additional payments earlier in the bill cycle with a credit card and still get your autopay discount if your payment method there is the debit card. When you are making that partial payment, you will want to make sure that the Update Autopay box is NOT checked, so you don't risk issues there.