You register once, independently of how many drones you have operating in the ’open’ or the ’specific’ category. Your registration will be valid for a period defined by your National Aviation Authority, after which you need to renew it.
However, you do not need to register yourself if your drone(s):
weighs less than 250g and has no camera or other sensor able to detect personal data; or
even with a camera or other sensor, weighs less than 250g, but is a toy (this means that its documentation shows that it complies with ‘toy’ Directive 2009/48/EC);
A drone is certified when it has a certificate of airworthiness (or a restricted certificate of airworthiness) issued by the National Aviation Authority. In this case, it requires a registration. A certified drone is needed only when the risk of the operation requires it. So certification is never needed for drones operated in the ’open’ category.
Relevant regulation: article 21 of EU regulation 2019/947.
Once registered, you receive a ‘drone operator registration number’ that needs to be displayed with a sticker on all the drones you own, including those privately built. You must also, upload it into the ‘Drone’s remote identification system’.
Regulatory reference: article 14 EU regulation 2019/947.