StopTech has gobs of info about brakes on their site. The bed-in FAQ has this to say about running 2 sets of pads on the same rotors.
FAQ #4: What precautions must be taken when switching from street pads to track pads?
If you are changing pad compounds, such switching from street pads to track pads, you need to remove all of the material on the rotor and replace it with a fresh transfer layer of material from the new pads. To be honest, rotors do not like to have different compounds used on them, and virtually all rotor and pad manufacturers recommend that you do not swap pad compounds on the same rotors. The reality is, however, that most customers don't have two complete sets of rotors, so here are our recommendation for managing compounds between track and street use. Note that diligent bedding-in is the key.
When switching from street pads to track pads, one needs to make sure that as much of the street compound is removed from the rotor as possible before aggressive track use. The risk here is that any street pad material remaining on the rotor will be subject to deterioration from overheating. This can ultimately cause severe vibrations due to uneven pad deposits (a smearing of the street pad material on the rotor face).
A common method for removing street pad material is to install the track pad prior to driving to the event. Because most track pads operate in an abrasive mode during regular street operation, driving them to the track will wear off any existing brake pad material en route. You will know when the street pad material is gone by the squealing noises coming from your brakes after a short while
FAQ #5: What precautions must be taken when switching from track pads to street pads?
Many people make the mistake of thinking that because they have a used set of pads in the past that the system does not need re-bedding when they are re-installed. Remember, the same material must be adhered to the rotor as the pad running against it for effective braking. Race pad material must be removed prior to street use.
Since you're not as likely to overheat the rotors on the street after a track event, over time the street pads will remove and replace the track pad material on the rotors naturally. However, the best solution where street pads are being put back into service after a track day is to follow the original bed-in procedure for the street pads after the swap.