Praise be to Allah.
Allaah has commanded us to fulfil our trusts properly, as He says (interpretation of the meaning):
“Verily, Allaah commands that you should render back the trusts to those, to whom they are due” [al-Nisa’ 4:58]
And the Messenger of Allaah (peace and blessings of Allaah be upon him) described betraying the ummah as one of the signs of hypocrisy, Allaah forbid. It was narrated from Abu Hurayrah (may Allaah be pleased with him) that the Prophet (peace and blessings of Allaah be upon him) said: “The signs of the hypocrite are three: when he speaks he lies, when he makes a promise he breaks it, and when he is entrusted with something he betrays (that trust).” Narrated by al-Bukhaari, 33; Muslim, 59.
With regard to this prohibition, it makes no difference if a Muslim betrays the trust of a fellow-Muslim or of a kaafir who has entrusted his wealth or property to him. Rather it is by being honest and trustworthy that he can give a good example of Muslims. Many nations entered Islam because of the trustworthiness and honesty of the Muslim traders. Conversely, if a Muslim is treacherous or tells lies, this puts people off Islam and turns them away from the path of Allaah.
Al-Shaafa’i (may Allaah have mercy on him) said:
If a Muslim enters daar al-harb (non-Muslim lands) in safety and gains some control over any of their wealth, it is not permissible for him to take anything of it, great or small, because if they have granted him safety then they are entitled to the same from him, and because it is not permissible for him to take anything from them when he is under their protection except that which he would be permitted to take from the wealth of the Muslims or of ahl al-dhimmah (non-Muslims living under Muslim protection). Al-Umm, 4/284.
Because you have agreed upon a specific salary with the company, it is not permissible for you to take anything extra without the knowledge of the company owner. The claim that they are not giving you what you deserve is no excuse. If you open this door, then every worker will make similar claims and rights and trusts will be lost.
Similarly it is not permissible for you to give discounts to anyone or to waive the price altogether. This money is not yours to do that with. You have to take the price in full no matter who the customers are.
So what you both have to do is to repent to Allaah by giving up what you are doing, regretting it and resolving not to do it again. You also have to give back to the company what belongs to it, namely whatever you took in addition to your salary and the discounts that you allowed to your acquaintances and friends.
See also the answer to question no. 14367.
And Allaah knows best.