All perfect praise be to Allah, the Lord of the worlds. I testify that there is none worthy of worship except Allah and that Muhammad is His slave and Messenger.
You made a mistake by taking money from the organization which you worked for without their permission, but you have done well in willing to return that money and be acquitted from sin.
You do not have to tell them what had happened or return the money openly; it is enough to give them back the money indirectly, such as by depositing it in the bank account of the company without their knowledge, or by similar means by which you would preserve your dignity and return the money to its rightful owners and get rid of its consequences.
The Prophet said, “The hand that takes is responsible for what it has taken until it returns it.” [At-Tirmithi]
The Prophet also said, “Whoever has wronged his brother, in his honor or anything else, he should ask for his pardon (before his death), as (in the Hereafter) there will be neither a dinar nor a dirham. If he has done some good deeds, a portion equal to his wrongdoing will be subtracted from them; but if he has no good deeds, he will be burdened with the evil deeds of the one he had wronged in the same proportion.” [Al-Bukhaari]
Therefore, you must hasten to return that money and be determined not to do this again.
Allah knows best.