Absolutely, you can choose which orders get sent over to FBA for fulfillment from other channels by following the steps below:
1. Navigate to Orders > Order Management > Paid - Ready To Ship Orders
2. Click 'view' next to the order you want to export to FBA
3. Click the green plus icon to the left of each item to confirm that the order has been allocated to your FBA warehouse. If it has not, change it to your FBA warehouse and then save.
4. Go back to the Paid Ready to Ship screen and select the orders you wish to fulfill via FBA by selecting the checkbox beside the order on the left hand side of the screen
5. Click the blue Export Orders button and choose Export Automated
6. Select your FBA warehouse from the drop down
7. Click the blue Export button