Beginner question regarding batteries' voltage/amperage
To get 12V you have to put them in series. This gives you 12V @ 4A. Placing them in parallel would give you double the current, i.e. 6V @ 8A. This is a bit tricky, however, because voltages of the two batteries have to be exact the same, otherwise a large current will run from one battery to the other. As safety measure you place small resistors in series with each battery.  

So you place them in series. A series resistor to get a defined lower voltage is never a good idea, because the voltage drop over the resistor will vary with the load. Use a voltage regulator, like LM7809 or LM317. The former will give you a fixed 9V, the latter is adjustable. This converts the 12V in to 9V out. If you connect the 9V, 1A device you'll have this 1A current automatically.