Custom commerce payment methods based on item
An administrator can add two payment transactions to an order using different payment methods from the admin > order > payment area.

However an end-user normally selects a single payment method from the radio button form during checkout.

To support multiple payment methods you may need to send the customer through the payment step of the checkout twice, each time with a different amount and a different payment method selected.

Payment method selection is controlled by Rules logic and can be configured there.
The order status controls whether it can be sent through checkout again so may need to be set to the relevant checkout status. 
The order amount to be paid may need to be set in custom code during the payment step process.