M2E Pro allows applying different prices for a product on a marketplace and Magento. Use the Price change option in eBay > Configuration > Policies > Selling Policy which allows adjusting an Item price on eBay. The following options are available:

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

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

Find more information about pricing for M2E Pro M1 and for M2E Pro M2.