Magento – how to sort specific payment method in 1st place in checkout page

One way to achieve this is in the file: app/design/frontend/base/default/template/checkout/onepage/payment/methods.phtml When looping over the selected methods add something like:

<?php if($_code == 'YOUR METHOD'): ?>
     <span class="no-display"><input id="p_method_<?php echo $_code ?>" value="<?php echo $_code ?>" type="radio" name="payment[method]" checked="checked" class="radio" /></span>
    <?php $oneMethod = $_code; ?>
<?php endif; ?>
    <label for="p_method_<?php echo $_code ?>"><?php echo $this->escapeHtml($this->getMethodTitle($_method)) ?> <?php echo $this->getMethodLabelAfterHtml($_method) ?></label>

Then add some JS at the bottom:

<script type="text/javascript">
//<![CDATA[
<?php if (is_string($oneMethod)): ?>
payment.switchMethod('<?php echo $oneMethod ?>');
    <?php endif; ?>
//]]>

In reality this is all that default magento template is doing to help the user select only a single option if one is set via the admin. However what I think might be happening in your case is that you have 2 methods available even though one may not be visible as a option. Adding this to the template will select that option by default and move to next step.

it seems like your system.xml may be missing this node in your extension

 <sort_order translate="label">
       <label>Sort Order</label>
       <frontend_type>text</frontend_type>
       <sort_order>100</sort_order>
       <show_in_default>1</show_in_default>
       <show_in_website>1</show_in_website>
       <show_in_store>0</show_in_store>
       <frontend_class>validate-number</frontend_class>
</sort_order>

hope this will be worth for you.