M2E Pro allows applying different prices for a product on the Channel and Magento. Use the Price Change feature in eBay/Amazon/Walmart > Configuration > Policies > Selling Policy which allows adjusting an Item price on the Channel.

You can add multiple price modifications for your products. For that, click Add Price Change, choose how you want to change the price, and enter the relevant value. The following options are available:

1) Absolute Value increase or decrease – increases\reduces Channel Item price compared to the corresponding Magento Product price by the specified number of units.

2) Percentage increase or decrease (%) – increases\reduces Channel Item price compared to the corresponding Magento Product price by the specified percent value.

Also, you can opt for Magento Attribute as a source of product price modification.

As for Amazon and Walmart, you can adjust the initial Price source value using the Price Change field. In this field, you provide an amount/percent value you want to increase/decrease the final Channel Price for. Add the “+” or “-” sign to the provided value depending on whether you need to increase or decrease the price.

In the Price Change field, you can also specify the Currency rate value by which the final Amazon/Walmart price will be multiplied.