In my Defender(that I use a JROK to play Defender and Stargate) I added an 2x20w external amplifier that drives the factory 6"x9" speaker on one channel and a powered sub-woofer on the other.
I fed the speaker out of the JROK to the input of the amplifier. Just make sure to turn the volume down on the JROK... I don't think it's output is enough to blow the input stage of the amp but it might.
The 6"x9" I replaced with a new one and I cut the hole in the cabinet larger since I was replacing the speaker grill.
The subwoofer adds ALOT to Defender. I'm not positive how much low frequency is in Sinistar but I'd assume it has a decent amount since it's a Williams game.
Oh, the subwoofer I use for a lot of my games is the Polk Audio PSW10. They go on sale quite often for ~$70-$80 and they have speaker level inputs so you can feed directly from either the external amplifier or the JROK board. I feed our Defender via the external amp.