The Command Secretary is lower-importance than any other job in Command. You only have access to the bridge and the fax machines, and in a crisis situation you'll be expected to communicate with CorpComm while the heads do the work of protecting and fixing the station. Outside of a crisis, you help command with whatever they need, which usually means filling out their paperwork and getting them snacks, if they even remember you exist.
This is your workhorse, the sole thing that sets you apart from the common Assistant (other than your nice suit and bank account). There's one fax machine found in the Meeting Room on the Bridge (which also passes for your office) and another in most Heads' offices and the Vacant Office. To use, just draft up paperwork with a pen and paper, insert it into the machine, swipe your ID for authentication, and choose a destination!
If you fax CorpComm a note scrawled in crayon asking for a party crate, the only way they'll react is by laughing at your face. At the bare minimum, try to make your paperwork look nice and official, either through the templates in Guide to Paperwork or through your own templates. Remember that you don't have any real authority on the station – whenever possible, try and get a relevant Head of Staff's signature or stamp on your documents before they get sent out.
The fax machine can send to any other fax machine on the station, which is of dubious utility considering that you also have the Command channel on your radio. More often than not, you'll be faxing either CorpComm or SolGov.
CorpComm is NovusCorp's Corporate Command. They're concerned with maintaining NovusCorp's PR and profitability by papering over problems as quickly as possible. Plainly, they're penny-pinching bureaucrats. However, CorpComm, being in charge of ship supply, is who to fax for unusual equipment (such as spare slime tasers in case of a horrible xenobiology accident) that isn't available in standard supply crates, or for emergency support.
SolGov is the local government, with authority over criminal law. Mostly, you'll be faxing them reports if someone is arrested for a high crime (this is technically the HoS's job, but they'll be happy to delegate it to you or their own secretary). They're also who to fax if the situation aboard the station gets bad enough to need actual military response greater than what your ship carries, but don't expect much; they move at the speed of government.
NovusCorp recommends keeping incidents involving potentially dangerous technologies purely in-house for PR reasons. If for some reason you need to publicly expose corruption in NC, you can fax SolGov, but NovusCorp will not be happy about it.
Aside from manning the Fax Machine, try and make yourself handy! You're basically an Assistant with Bridge access, so offering to ferry things between departments is a good use of your time. Offer to bring lockboxes from R&D to the HoS to unlock! Help the HoP distribute improved access by moving around ID cards! A good Command Secretary can make the life of the Command Staff much smoother and more convenient.