Praise be to Allah.
Stealing is a major sin, and we praise Allah for having guided and enabled you to repent. So strive hard to make sure that your repentance is as prescribed in Islam, and do not respond to evil with evil, or find false excuses based on misinterpretation. The fact that your boss broke his promise to you does not justify your stealing and continuing in it, especially since you state that he only did that because of what you stole from them.
You should try hard to find out how much you stole from the company. If you are not able to find out exactly how much it was, then work out what you think you most likely took from them unlawfully, then return it to them. Allah, may He be glorified and exalted, says (interpretation of the meaning): “So keep your duty to Allah and fear Him as much as you can” [at-Taghaabun 64:16].
Shaykh as-Sa‘di (may Allah have mercy on him) said:
This verse indicates that if a person is unable to do an obligatory deed then it is waived in his case; if he is able to do some of what is enjoined and unable to do some of it, then he should do what he is able to do, and what he is unable to do is waived in his case. The Prophet (blessings and peace of Allah be upon him) said: “Whatever I instruct you to do, do as much of it as you can.” This Islamic principle covers innumerable minor issues.
End quote from Tafseer as-Sa‘di (p. 868).
As you have returned half of what you took from the company unlawfully, you have done well, and you should strive hard to return the other half.
You do not have to inform the owner of the company of the situation or of what you have done, or of what you intend to do, if you fear that this will result in bad consequences or fitnah, or if it is difficult for you to tell him and you are afraid that there may be some negative consequences for yourself, because Allah loves to conceal people’s faults. Rather what you must do is restore rights to those to whom they belong, no matter how that is done, so long as it is permissible; then you must repent to Allah, may He be glorified and exalted, and ask a great deal for forgiveness.
Righteous deeds such as praying, fasting, giving charity, offering supplication (du‘aa’), remembering Allah (dhikr), and so on, with the intention of repentance and striving to restore people’s rights, will be accepted in sha Allah. In fact they are part of repentance as enjoined. For a righteous deed to be accepted, it is not essential that the doer should have no sin, major or minor, on his record, and committing a major sin does not necessarily erase what the doer has to his credit of righteous deeds, unless that pertains to a particular case concerning which there is a text.
Rather confusion may arise concerning acts of worship that are connected to that sin; in such cases the sin will have an impact on the acceptability of the deed, and may cause it to be rejected and not accepted.
This case is similar to the case of repentance from sin whilst persisting in other sins.
Ibn al-Qayyim (may Allah have mercy on him) said:
Is repentance valid if one repents from one sin whilst persisting in another sin? That is a matter concerning which there are two scholarly opinions … My view concerning this matter is that repentance from one sin cannot be valid when one is persisting in another sin of the same type. But in the case of repenting from one sin when still committing another that has nothing to do with it and is not of the same type, that repentance is valid. For example if a person repents from dealing in riba but has not repented from drinking alcohol, for example, his repentance from riba is valid. But if a person repents from dealing in riba al-fadl (when similar commodities are exchanged unequally, such as one measure of dates for two measures of a different quality of dates) but he does not repent from riba an-nasee’ah (when the amount of debt is increased when the debtor is unable to pay off the debt at the appointed time and requests extra time in which to pay it off), and he persists in it, or vice versa; or he repents from smoking hashish but persists in drinking alcohol, or vice versa – in such cases his repentance is not valid. This is like one who repents from committing zina with one woman but is still committing zina with another woman and has not repented from that; or he has repented from drinking wine but he is still drinking other intoxicating drinks. In such cases he has not really repented from sin; rather he has merely moved from one type to another. This is unlike one who turns from one sin to another that is of a different type.
End quote from Madaarij as-Saalikeen (1/273-375)
With regard to these things that you bought with that stolen money and gave in charity to the poor, you should understand that your giving these things in charity to the poor is not valid, regardless of whether you gave the items themselves or the amount for which you bought them, because that is haram wealth that must be returned to its rightful owners. It is not permissible to give it in charity because Allah is Good and does not accept anything but that which is good.
As you intend to return the money in full to its owners, then you have done well, and you should hasten to return it.
It is not prescribed for you to pray istikhaarah about returning this wealth to its owners, and you do not need to do this prayer with regard to the possible way of returning it, because returning it when you are able to do so is obligatory, and it is not prescribed to pray istikhaarah about something that is obligatory. Shaykh Ibn ‘Uthaymeen (may Allah have mercy on him) said: One should not pray istikhaarah about something that is obligatory, because Allah has ordained that it is obligatory.
End quote from al-Liqa’ ash-Shahri (4/135).
See also the answer to question no. 11981
But if you are hesitant about two possible ways of returning it, and you do not know which of them is better and closer to concealment, then istikhaarah may be appropriate, because you are uncertain as to the choice between two things that are prescribed, and you cannot work out which of them is better.
And Allah knows best.