The primary device is used to track the GPS for My Location alerts and controls and all merchant and threshold alerts will be sent to the primary device. All devices that have registered a particular card can view or change the CardValet settings for that card.
Controls (including the On/Off setting) are set at the card level, so the last update to a control will be honored regardless of which phone was used to make the change. Alerts are set at the device level, so each primary device will receive alerts that were set up from that particular device. The primary device can be re-set by accessing Settings>Primary Device.