Add Stripe's processing fee and your platform application fee as metadata

metadata.php

<?php 
$charge = \Stripe\Charge::create(array(
  "amount" => $db->amount, // The total amount to charge the customer, in cents
  "currency" => "usd",
  "source" => $token, // The token submitted from Checkout or Stripe.js
  "application_fee" => $application_fee,
  "destination" => $db->connected_account_id, // The account ID, retrieved from your database
  "metadata" => array(
    // Calculate Stripe's processing fee based on the total charge amount
    "stripe fee" => ($db->amount/100 * .029 + .30) * 100, 
    // The remainder of your application fee is the commission for your platform
    "application fee" => $application_fee - (($db->amount/100 * .029 + .30) * 100)
  )
));