In case you use the same email while ordering the Update Service as you used for purchasing Store Manager, your updates will be applied automatically to your Primary license.
In case you use a different account/email, you need to apply them manually. After purchasing the Update Service you will receive a license key which you need to apply to your existing Store Manager license with the help of the Licensing Tool.
Alternatively, you can download the latest updates from your account in the eMagicOne License Management Tool.