Firstly: 

If your work does not involve dealing with riba or approving it or helping with it, or dealing with other haraam things apart from riba, then it is permissible work and there is no sin on you if you continue it, even if the company takes riba based loans or pays riba. But it is better to leave this job and work for a company that is far removed from this great evil, because it is established among the scholars that it is makrooh to engage in buying and selling and renting etc with persons whose wealth includes haraam wealth. 

Secondly: 

It is not permissible to write down riba or to document it. The one who does that is cursed by the Messenger of Allaah (peace and blessings of Allaah be upon him), as Muslim (1598) narrated that Jaabir (may Allaah be pleased with him) said: “The Messenger of Allaah (peace and blessings of Allaah be upon him) cursed the one who consumes riba, the one who pays it, the one who writes it down and the two who witness it, and he said: ‘They are all the same.’” 

Following up on these documents and supervising them is haraam, because it is cooperating in sin and transgression, and approving of evil. Allaah says (interpretation of the meaning): 

“Help you one another in Al‑Birr and At‑Taqwa (virtue, righteousness and piety); but do not help one another in sin and transgression. And fear Allaah. Verily, Allaah is Severe in punishment”

[al-Maa’idah 5:2]

What you have to do is advise those who are in charge of this company to give up this great evil. If they respond, then praise be to Allaah, otherwise you must avoid recording and documenting riba, and keep away from everything that involves helping in sin or approving of it. 

And Allaah knows best.