Hi,

Based on Paymate module, I think somehow AlertPay module needs to change this code from:
zen_draw_hidden_field('ap_amount', number_format($order->info['total'], 2, '.', ''))

to something like:
zen_draw_hidden_field('ap_amount', number_format(($order->info['total'] - $order->info['']))

I am not sure if this would work, give it a go and let us know?