I imagine that you have different IP-numbers on eth0 and eth0:1, so to use different rules you have to look at the IP-numbers also, i.e. something like this (this is just a short example)
$IPT -A INPUT -i $INET_ETH -d $INET1 -j ip1_from_inet
$IPT -A INPUT -i $INET_ETH -d $INET2 -j ip2_from_inet
$IPT=/sbin/iptables, $INET_ETH is the ethernet interface, i.e. eth0, $INET1 and $INET2 are the two different IP-numbers of eth0 and eth0:1, both jump of to two different chains with different rules in them.