If the simple parts are given by machines, then in general there is no canonical way of composing them into a machine for the composed program. You have to construct a new machine from the machines for the parts. An example is the sequential composition of two functions with logarithmic space usage. You cannot just use run one machine after the other, but you have to modify both machines and then build a new machine that contains them in the right way.
Of course, one may use systematic constructions to combine simple machines into more complicated ones. But this amounts to the implementation of a programming model.