where to put includes

[JRough]

I have this at the top of the file

include './includes/config.inc.php';
include $include_path.'dates.inc.php';
include $include_path.'auction_types.inc.php';
include $include_path.'countries.inc.php';
include $include_path.'datacheck.inc.php';
include $include_path.'wordfilter.inc.php';
include $include_path.'converter.inc.php';

I have some other includes inline with mysql queries:

include "header.php";

$_SESSION["sessionVars"]=$sessionVars;
include "header.php";
include phpa_include("template_menu_php.html");
include phpa_include("template_sell_preview_php.html");
include "footer.php";
exit;
}
$query = "SELECT * FROM PHPAUCTIONXL_invitedbuyersrows WHERE list_id=
$v";
$resi = @mysql_query($query);
if(!$resi) {
MySQLError($query);
exit;
} else {
while($user = mysql_fetch_array($resi)) {
$query = "SELECT name,email FROM PHPAUCTIONXL_users WHERE id='".
$user["buyer_id"]."'";
//print $query."<br />";
$resu = @mysql_query($query);
if(!$resu) {
mySQLError($query);
exit;
} elseif(mysql_num_rows($resu) 0) {
$BUYER_EMAIL = mysql_result($resu,0,"email");
$BUYER_NAME = mysql_result($resu,0,"name");
include $include_path."invitation_email.inc.php";
}
}
}
}
}

What I want to know is how to organize it. I don't have a template
and I don't know what one is. How can I take all the includes out and
put it on one page? Is that what this directory is for. How can you
know which includes need to be in the directory and which includes
must be in-line?:
include './includes/config.inc.php';

Thanks,