Letting the flight attendants know you will be boarding with your service animal in the pre-boarding process can help make the situation easier. Informing them of any previously approved request for seating, or requesting seating appropriately spaced for you should be done then. In addition, asking permission to pre-board so you and your service animal are settled down and out of the way before it becomes hectic should benefit the entire situation.
Flying with a service animal should not be an exhausting and frustrating experience. To reduce the chances of this happening, understanding the process unique to your airline as well as the general requirements can benefit everyone involved.