Hi,
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 documentation.
In your case, you need to register the web part e.g.:
<%@ Register Src="~/CMSWebParts/Localization/languageselectionwithflags.ascx" TagName="languageselectionwithflags"
TagPrefix="cms" %>
and then use it on appropriate place:
<cms:languageselectionwithflags runat="server" ID="wLS" />
Best regards,
Juraj Ondrus