How you inform the registrar that the domain is owned by a company is a practical issue and therefore off-topic for this site.
From the legal perspective, all companies ultimately have to act via a natural person.
In england-and-wales, the applicable rule is found in Section 43(1) of the Companies Act 2006:
Under the law of England and Wales or Northern Ireland a contract may
(a) by a company, by writing under its common seal, or
(b) on behalf of a company, by a person acting under its authority,
express or implied.
"Express" authority to enter into contracts is derived from the company's constitution which sets out the powers and limitations of the directors (including any power to delegate authority to other people). Note however that the other party to the contract, if they acted in good faith, can rely on the contract even if the person purporting to act on the company's behalf was not authorised to do so. This rule is found in Section 40.