If it has speaker level inputs, you would just run speaker cables from the new amp.
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Given the very limited power output of the original Janus amps ( something like 60 watts if i remember correctly ), i would think that you would be MUCH better off with a good quality external amp. Having said that, i don't know if the OEM Janus amps had any type of proprietary EQ built into them to compensate for deficiencies in the speaker / cabinet design. As long as the Janus has been around, i'm sure that someone has "gutted" one and gone to auxillary amplification. Hopefully, they'll be able to share first hand insight with you. Sean