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