With such a vague question, it is difficult to give more than a vague answer, but here are some thoughts. Monoids are very similar to groups (in precisely the same way as commutative rings are a lot like fields). How do we study any difficult group? We study its representations. To my knowledge, this is the best approach to studying monoids as well. In terms of your question, one would hope that, with a given monoid in mind, one would have a description of objects the monoid acts on along with the associated actions.
More generally, most methods of attack one has for groups generalize to monoids, there might just be less one can say for the general case.
One can go further; a standard trick when dealing with monoids is to look at their groupification (Grothendieck group), understand the structure of the group and see what data can be reclaimed about monoid (similar to studying an integral domain by looking at its field of fractions).
In general, I can't imagine that the isomorphism type of the monoids you are looking at are all that interesting in the same sense that isomorphism types of abelian groups are not all that interesting. The interesting question is how they arise as parts of other structures (knowing the isomorphism type of a finitely generated abelian groups is not all that exciting, knowing which ones arise as the rational points on an elliptic curve, and HOW they arise is far more noteworthy).