How do I make sure that the Shopify order has the same total as the Shopee order?

The app has a lot of options to customize the import of the Shopee order into a Shopify order. If you want the Shopee order to have to same amount on the Shopify order, I recommend enabling all the options

If you have Shopify VAT and Shopify Shipping enabled (see screenshot):

The app does not control this. You will have to disable this yourself by disabling VAT on Shopify and the Shipping charges. Once you disable both and enable all the app's fees options your imported orders will have the same total as your Shopee orders.