If you have two Government Gateways, you can use one to register for Self Assessment and discard the other.
It wouldn't matter which one unless you have already registered for an online service with one of the IDS.
Once you have completed the registration, we will send you a UTR and you will be able to access Self Assessment through the Business Tax Account.
The SA109 can online by filed by paper, unless your purchase third party software.
Self Assessment commercial software suppliers