Should I cover the main or the branch panel?

Cover both and consider that a recommended minimum of two levels of protection is optimum. The main panel or service entrance surge protective device (SPD) provides the first line of defense against large externally generated transients stepping them down to safe levels. These externally generated transients include those caused by lightning, downed power lines and similar distribution problems, as well as noisy electrical neighbors. The main panel device also calms the internally generated transients which reach it from loads directly connected to it and from connected sub or branch panels. The main panel device prevents the redistribution of these internally generated transients. Branch panel SPDs handle the surge remnants which may remain after a massive hit at the main panel has been stepped down. Additionally, branch panel SPDs prevent transient cross contamination between the various circuits and their connected loads. Point-of-use and individual equipment protection (always consider AC and signal protection) isolates the protected system from transient activity on the same circuit.