In /skin1/mail/html/order_invoice.tpl
look for :
Code:
<td align="center"><br /><br /><font style="FONT-SIZE:12px">{$lng.txt_thank_you_for_purchase}</font>
add below it:
Code:
<br />
{if $order.payment_method eq "Finance"}
<p>Add your Message here !!</p>
{/if}
obviously you will need to change both the $order.payment_method value & the text to your own requirements
hope that helps you anyways