If I understand your question correctly, you ask about the difference between an atom and a monad - is that right?
If it is, then the major difference between them is probably the fact, that a monad is not pure matter as atom (Epicureans were matterialists: even souls they considered to be build of atoms, just of some different type). I don't want to make a mistake, but I am quite confident that a substance in Christian philosophy is a term generally not associated with matter.
But there are other differences: I assume that Epicurus concept of atom is familiar to you and the Leibniz's monads just cause confusion. (Indeed, monadology is rather odd metaphysical system.) I would recommend those articles about monads, they describe the idea of a monad quite well:
Note the biggest differences:
- Atoms are pure matter, whereas monads are not.
- Atoms are connected with other atoms, whereas monads can not interact
between them (monad "has no doors or windows")
- Atoms are what is the world build of in a sense as bricks are what a
wall is build of, whereas monads are complete beings - they all are
the parts of the universe and in every of them there is a
reflection of the universe in which it appears as if they could interact.
And some differences according to particularly Epicurus' concept of atoms:
Atoms are not the smalles parts of the universe - they are made of minima, whereas monads are indivisible.
Atoms are not fully determined - there are some random movements of atoms called clinamen (greek: parenklisis), whereas monads... well, they are determined in a specific way and it is all quite complicated (the articles I recommended should put some light onto it).
On the other hand, there is no reason why couldn't the matter (not substance) be made of atoms in Leibniz's concept: I cannot though provide evidence that he has actually thought so and I am sure that it is not an important part of his philosophy (the atom concept in Epicurus' philosophy was developed for his ethics - and a similar role in Leibniz's philosophy certainly play monads).