A notary should never notarize a signature not made in the notary's presence when notarizing in-person documents! This is the most important rule to protect a notary from legal liability.
A notary is to serve any person who makes a lawful and reasonable request for a notarization.
A notary is an impartial witness to a transaction.
A notarization does not prove truthfulness of the contents of a document, nor validate a document and render it legal.
A notarization provides verification of a document signers willingness to sign, his competence to sign, and that the signer is, indeed, the person identified by the signature.
If a notary has any doubt about a signers identity, it is best not to notarize that signature.
Notaries are encouraged to utilize a credible witness when in doubt about a persons identity. A credible witness is any person who personally knows the signer of a document. The notary should likewise personally know the credible witness. The credible witness may, under oath from the notary, attest to the identity of the document signer. Remember, the credible witness should be impartial to the transaction being notarized.
When it comes to notarizing your own signature you need to keep in mind SDCL 18-1-12.2. It is a Class 1 misdemeanor for a person to affix a signature to a document as a notary public when the person has also signed the document as a party to the transaction proceeding.