All perfect praise be to Allaah, The Lord of the Worlds. I testify that there is none worthy of worship except Allaah, and that Muhammad is His slave and Messenger. We ask Allaah to exalt his mention as well as that of his family and all his companions.
What is known as overdraft is nothing but a loan with Ribaa (interest and usury), and it is known that Ribaa is one of the great major sins. Allaah Says (what means): {O you who have believed, fear Allaah and give up what remains [due to you] of interest, if you should be believers.}[Quran 2:278]. Furthermore, the Prophet said: "Ribaa consists of seventy kinds or doors of evil, and the least of them (in severity) is similar (in sin) to one having sex with his own mother". [Ibn Maajah].
Therefore, the said company should stay away from this obnoxious sin.
Anyway, it is permissible for you to work for it since most of its money come from lawful sources, but it is better to avoid working for it and look for another work with a company whose money are not mixed with forbidden income.
For more benefit, please refer to Fatwa 82032.
Allaah Knows best.