One addendum: I had to insert this additional code to make sure the category pages that linked through index.php didn’t also redact the categories I wanted to eliminate from my first page. See below:
<?php
$homepage = "/";
$currentpage = $_SERVER['REQUEST_URI'];
if($homepage==$currentpage) { query_posts($query_string . "&cat=-3,-5"); }
//Block categories 3, 5 from main page
?>
