Create a notice on the Payment Methods section of the My Account page. Works best for instructing customers that changing the 'Default method' will NOT change any active subscriptions without also checking the checkbox.

notice__before_payment_methods.php

<?php

function notice__before_payment_methods( $has_methods ) { 
    wc_print_notice( __( 'In order to effectively change the payment method on ALL of your subscriptions, you must check the checkbox on the next page after clicking \'Add payment method\'.<br><br>You can also change the payment method on ONE subscription by visiting the individual subscription in the \'Subscriptions\' tab. More info can be found <a href="https://docs.woocommerce.com/document/subscriptions/customers-view/#section-11">here</a>.', 'woocommerce' ), 'notice' );
};
add_action( 'woocommerce_before_account_payment_methods', 'notice__before_payment_methods', 10, 1 );