Partner took money from the company without his partner’s knowledge

Firstly: 

Cheating or treachery is not a characteristic of the believers; rather it is a characteristic of the hypocrites. The Prophet (blessings and peace of Allah be upon him) said: “There are four things, whoever has all of them is a pure hypocrite and whoever has one of them has one of the characteristics of hypocrisy, until he gives it up: When he speaks he lies, when he is entrusted with something he betrays that trust…”

Narrated by al-Bukhaari, 33; Muslim, 88 

According to the hadeeth of Abu Hurayrah (may Allah be pleased with him), he said: “The adulterer is not a believer at the time when he is committing adultery; the thief is not a believer at the time when he is stealing; the one who misappropriates something from the war booty is not a believer at the time when he is misappropriating it, so beware, beware.” Narrated by Muslim, 86. 

An-Nawawi (may Allah have mercy on him) said: “Misappropriating something from the war booty” is a kind of betrayal. End quote from Sharh Muslim, 2/45. 

Betrayal is a blameworthy characteristic; the one who does it is not beloved to Allah, may He be exalted: “Verily, Allah does not like anyone who is a betrayer of his trust, and indulges in crime” [an-Nisa’ 4:107]. And there are other verses which indicate that this characteristic is hateful to Allah, may He be exalted, and contrary to sound human nature. 

The author of az-Zawaajir regarded it as a major sin. He (may Allah have mercy on him) said:

The one hundred and eighty-seventh major sin is devouring wealth by means of corrupt transactions and all kinds of haraam earnings. Allah, may He be exalted, says (interpretation of the meaning): “O you who believe! Eat not up your property among yourselves unjustly” [an-Nisa’ 4:29]. Ibn ‘Abbaas said: This refers to what a person takes without giving something in return. That is because consuming another person’s wealth unjustly includes everything that is taken unjustly, whether it is by unlawful means such as plunder, treachery or theft, or by means of a plot and cheating, such as that which is taken by means of false contracts.

End quote from az-Zawaajir bi Iqtifraaf al-Kabaa’ir, 2/106 

It was narrated that Ibn Mas‘ood (may Allah be pleased with him) said: The Messenger of Allah (blessings and peace of Allah be upon him) said: “Whoever deceives us is not one of us, and plots and deceit lead to the Fire.” Narrated by at-Tabaraani in al-Kabeer and as-Sagheer with a jayyid isnaad; and by Ibn Hibbaan in his Saheeh. See: Saheeh at-Targheeb wa’t-Tarheeb by Shaykh al-Albaani (may Allah have mercy on him), 2/159 

Secondly: 

You said: “I noticed that he was cheating me…” 

Our response is that the basic principle concerning the Muslim is that he is honest, unless there is proof that he is otherwise. If there is no such proof, then the basic principle remains that he is honest and innocent of treachery. 

Based on that, what you must do first of all is repent sincerely to Allah, may He be exalted; see the answer to question no. 46683. 

Thirdly: 

You must return the money that was taken unlawfully, and you will not have done all that is required of you except by returning it, unless you tell him what has happened, and he pardons you, in which case it does not matter. If he accepts what you say about having taken some of the money, without asking how much you took, and forgives you, that is good enough.

some of the money, without asking him to tell you how much it was and?? 

You should also pardon him in the same manner, without asking him how much he took. 

You can also return the money without telling him; if you do not know how much it was then you have to do your best to work it out and give what you think most likely is the amount you took. For more information, please see the answer to question no. 40019 

And Allah knows best.