How can a person who fell short in his work make amends for his sin?

The employee is obliged to do his work as is required of him, so that he
will be entitled to the salary that he takes in return for that work. 

If
there is any shortcoming in his work, then the basic principle is that he is
not entitled to take the salary in full, because he did not do the work in
the manner required. 

It
says in Fataawa al-Lajnah ad-Daa’imah (vol. 1, 15/154): What is
required of the one to whom work has been given, in return for which he
receives a salary, is to do the work in the manner required. If he falls
short in that without a legitimate excuse, the salary that he takes is not
permissible for him, because he is taking it without having done his work
properly in return. 

Based on that, you have to repent and not repeat what you have mentioned.
You must be honest in doing the work that has been given to you to do, and
give ing charity whatever is equivalent to what you took of the salary with
no legitimate excuse. End quote. 

Based on the above, the first thing that anyone who does any such
shortcoming must do is repent to Allah, may He be exalted, from his
shortcoming. 

He
does not have to get rid of the books that he bought with this salary, or
give them away; rather he may make use of them. All that is required of him
is to get rid of the salary that he received, commensurate with the degree
to which he fell short. If he fell short in half of his work, he should get
rid of half of that salary, and so on. 

He
should only get rid of it by returning it to the workplace to which it
belongs, if that is possible; otherwise he may donate it to charitable
causes. 

Note: some countries have set up accounts for employees of the state who
fell short or took anything from public funds, to pay it back. If someone is
in a country where such accounts and schemes have been set up, and he falls
short in his work and he is employed by the government, then he may return
the money to that account and thus will have discharged his duty. 

We
ask Allah to help us all to shoulder responsibilities and render back trusts
in the most perfect manner, for He is able to do that. 

And Allah knows best.