How to Manually Add Store Credit Option to the Magento Checkout

Magecredit should automatically integrate into your shopping cart. In the event that it doesn't, please see our Display Troubleshooting page.

In general, Magecredit requires the store credit field to represent "use" or "don't use". This is done basically by just setting the ['payment']['use_customer_balance'] request value to 1 if you want to use store credit, or 0 to not use store credit after a quote/order total update - just like Magento's core checkout does it. Assuming the 3rd party checkout module does not hinder any observers or checkout blocks, Magecredit will observe the quote and update the total.
You can look at app\design\frontend\base\default\template\customerbalance\checkout\onepage\payment\additional.phtml for reference.

Magecredit requires the methods_additional block to appear within the payments block in the checkout. That means you should add <?php echo $this->getChildChildHtml('methods_additional', '', true, true); somewhere in your checkout phtml files. Likely this will be in your payments.phtml file and look like this when it's done:
<form action="" id="co-payment-form">
    <?php echo $this->getChildChildHtml('methods_additional', '', true, true); ?>
    <fieldset>
        <?php echo $this->getChildHtml('methods') ?>
    </fieldset>
</form>