yes in series so theres 4.5v going through the controller. this gives you about 2x the range and it will allow you to charge a dual battery car if you ever want to do that which i highly suggest.
and to answer your question towards kwibb yes if there isnt a cripple cap in the transmitter, there may be one on the pcb. it is really really small and even if you are skilled at solder removal i would suggest not risking destruction of a perfectly good car. if you still want to do it check out
www.questformadness.com
they have detailed instructions on what to do.