Have a look at the documentation for ode45().
Generally speaking you provide a function handle to a function in two parameters, the first of which is time. The second parameter is generally a vector the same length as the number of derivatives involved, and provides the boundary condition values at the initial time (I do not know yet how to handle the situation where the boundary conditions are stated in terms of different times.) The function should return the derivatives at the current time.
See the documentation for examples.
