I think you mean ASPX templates - you can add it as any other web part. It should be worthy to go through the ASPX templates development model
In your case, you need to register the web part e.g.:
<%@ Register Src="~/CMSWebParts/Localization/languageselectionwithflags.ascx" TagName="languageselectionwithflags"
and then use it on appropriate place:
<cms:languageselectionwithflags runat="server" ID="wLS" />