if it's the bose system, the amp is fitted to a plastic tray underneath the parcel shelf.
Essentially, the "speaker" outputs from the bose badged head unit are line level (0.7 volts or thereabouts) - these connect to the amp which filters and amplifies them, then feeds the amplified signal back to the speakers.
You therefore have three main choices that come to mind:
1) remove the amp, connect input to output for each speaker connection at the plug which connects to the amp - this is what was done on my old miggy - it works but there is then very little signal sent to the woofers on the parcel shelf so the bass is a bit lacking
2) make a wiring loom to feed the pre-out signal from the replacement head unit into the "speaker" connections on the ISO plug, these are generally higher than 0.7V but hopefully will be low enough to not cause the amp to trip out. I proposed this but never implemented it on my old miggy - but the opinion at the time was that this will work OK - and sound significantly better than option 1 !!!
3) as per 1) - but connect an after-market amplifier between input and output ...