Hi Michael Park,
If you add the logic to your master page code behind, you actually will hard code it which is not good practice. You should use user or custom controls. For Sitefinity it does not matter from where you will upload the file. In both cases it is located under App_Master directory. However the way that suggest for changing the theme is creating a custom class that inherits from Internal page and then overriding OnPreInit method.
MyInternalPage : InternalPage
IPageTemplate newTemplate =
You need to override GetMasterPageName, GetTheme and AddPageControls methods and set newTemplate.Theme.
Finally you need to replace the default internal page and set the newly created
<%@ Page Inherits="Telerik.Sitefinity.Samples.MyInternalPage" MasterPageFile="~/Sitefinity/Dummy.master" %>
the Telerik team