Typically, a startup would designate only certain personnel who are in positions of responsibility to sign the NDA on behalf of the company. The CEO and people on senior staff are often among the people who can sign the NDA on behalf of the company. This is made clear typically by stating the person's title and company name right on the signature line. Some people prefer to make it even more explicit by making the signature line look like this:
For [Company name]
__________________________ (signature line)
Name of person
Title of person
If the signature line does not specify the company name, then you are signing the NDA as an individual. This means that the NDA only protects the other side from information disclosure from you, the person, not your startup.