Pupoz, be aware that dynamcal systems is a huge field, and there are many, many things you can call a dynamical system besides a system of coupled nonlinear ODEs. For example, in my diss I (following Conway and de Bruijn) studied the space of Penrose tilings as a tiling dynamical system; as was first recognized (independently) by Conway and de Bruijn, such dynamical systems can be fairly characterized as a kind of geometric realization of number theoretic phenomena in the theory of simultaneous rational approximation!
You might want to spend some time with the wonder "picture book" by E. Atlee Jackson, Perspectives of Nonlinear Dynamics (two volumes), plus the fine textbook by Hilborn, Chaos and Nonlinear Dynamics. Together these should provide a solid appreciation of the scope of modern dynamical systems theory.
I could add numerous references on ergodic theory and symbolic dynamics, the most abstract branch of the field of dynamical systems theory. These are mostly at the graduate level, but if you want to understand Markov chains (you mentioned "transition functions") at a combinatorial level, symbolic dynamics is the way to go, and you'll need ergodic theory in order to understand the interaction between combinatorial, topological, and probabilistic structure in a Markov chain. Well, let me mention one undergraduate textbook: the first half of Lind and Marcus, Introduction to Symbolic Dynamics and Coding should give a good introduction, but there's a lot more to this.