One possible problem you may have with 2 independent devices updating the same channel is that thingspeak only allows 1 update every 15 seconds so if your 2 devices attempt to update the same channel within 15 seconds of each other then the second update will fail. It may be best to create separate channels then graph the combined data using the Matlab Visualisation app.
You can use the same write API key for the two devices although you will still have the problem above.
If you explain a bit more about how your graphs are broken it may help.