SP Foundation 2010 - programmatically set custom master page in site template

I created a site template from a one page site that uses a custom master page for the front end, the default master for the back end. When a new site is created from the template, the front end page reverts to the default master page and I have to manually correct it in SP Designer. Is there a way to switch the template for (any) site pages to the custom master without any manual interaction? This is the part that needs to change:

<%@ Page language="C#" MasterPageFile="~masterurl/custom.master"      Inherits="Microsoft.SharePoint.WebPartPages.WebPartPage,Microsoft.SharePoint,Version=14.0.0.0,Culture=neutral,PublicKeyToken=71e9bce111e9429c" meta:progid="SharePoint.WebPartPage.Document" meta:webpartpageexpansion="full"  %>