CodeBehind
Needs to be compiled and the compiled binary is placed in the bin folder of the website.
<%@ Page Title="" Language="C#" MasterPageFile="~/YourMasterPage.Master" AutoEventWireup="true" CodeBehind="YourFile.aspx.cs" Inherits="YourPage" %>
CodeFile
You provide the source file with the solution for deployment and .NET compiles the code when needed.
<%@ Page Title="" Language="C#" MasterPageFile="~/YourMasterPage.Master" AutoEventWireup="true" CodeFile="YourFile.aspx.cs" Inherits="YourPage" %>