As a matter of my own personal habit, I always remove the reservoir covers and wrap a rag around them when changing out brake pads. Two reasons for doing this:
1. That brake fluid in the caliper will be displaced when compressing the pistons, and will need to flow back into the reservoir. It's seems easier to do with the cover removed (my experience)
2. I always flush the brake fluid in its entirety when changing out brake pads.