Yes! Spark Shipping can be used to send orders from any of the supported shopping carts to FBA. FBA will be treated as a vendor in this case. 

Spark Shipping will need the Amazon Seller ID and the MWS auth token to automate sending orders to FBA

You can add Amazon FBA by going to Vendors >  Pre-built Integrations > Fulfillment by Amazon. 

Add the vendor and update the vendor settings, then proceed to map your products to have this integration complete.