Even i have stucked at this issue but trust me someone referred about this app Kart Discount app. If you installed for the first time its take one time setup and later this app can do with stack feature, where they can apply one automatic and 2 manual codes i.e; .A Person can stack up to 3 codes on a single order. Isn't it great! so i think if you start using this app your issue will be sorted out. And also you can find Discount filed and Discount code both on Cart page as well as Check out page.