All regulatory interactions (inhibition, activation, etc.) should be indicated as an effect of a species on a reaction. The resulting diagram is called a process diagram and it unambiguously translates to a system of differential equations.
You will recall that an SBML species is a molecule or molecular complex in a place or compartment and a SBML reaction is a process (biochemical, transport, or binding)
I blogged about this a few years ago and the blog post is here: