I just have the following code in my skin1/mail/html/order_invoice.tpl
Code:
{*** Show payment information for queued invoices***}
{if $order.status eq "Q"}
<TR>
<TD colspan="3"></TD>
</TR>
<TR>
<TD width="45%" height="25">{$lng.lbl_order_payment_instructions}</TD>
<TD colspan="2" width="55%"></TD>
</TR>
<TR>
<TD bgColor="#000000" height="2">[img]{$ImagesDir}/spacer_black.gif[/img]</TD>
<TD colspan="2">[img]{$ImagesDir}/spacer.gif[/img]</TD>
</TR>
{if $order.payment_method eq "Money Order" || ($order.payment_method eq "Cheque (manual processing)")}
<TR>
<TD colspan="3">
{$lng.lbl_order_chq_mo_instructions}</TD>
</TR>
{/if}
{if $order.payment_method eq "Direct Deposit"}
<TR>
<TD colspan="3">
{$lng.lbl_order_dd_instructions}</TD>
</TR>
{/if}
{if $order.payment_method eq "Phone Ordering"}
<TR>
<TD colspan="3">
{$lng.lbl_order_phone_instructions}</TD>
</TR>
{/if}
{if $order.payment_method eq "Fax Ordering"}
<TR>
<TD colspan="3">
{$lng.lbl_order_fax_instructions} {$config.Company.company_fax}
</TD>
</TR>
<TR>
<TD colspan="3">Cardholders Name (as shown on card):____________________________________________________
</TD>
</TR>
<TR>
<TD colspan="3">Card Number:___________________________________ Expiry Date:______/___________
</TD>
</TR>
<TR>
<TD colspan="3">CVN Number (optional):_________ Cardholders Signature:___________________________________</TD>
</TR>
{/if}
{/if}
Which will depending on the payment type selected display instructions in the existing 'Payment Instructions' section. It will only do this for invoices with a status of queued.
I don't know how your version handles the payment but you might be able to apply the same principle to your invoice template? Hope that helps.