BOSE amp trigger is in the yellow block and is likely to be a grey wire with green stripe down it.
As people have said - your new head unit isn't turning the BOSE amp on. The BOSE amp is like an external amp on an after market setup only the trigger wire in the yellow block shuts down the internal amp on the factory headunit and turns on the BOSE amp.
The problem you're going to have is that your new pioneer unit isn't going to understand there is an external amp in the loop and will run its internal amp, so you're effectively amplifying the signal twice - so it could lead to poor sound quality / boomy audio and extremely loud music at rather low volumes. Thus you may - depending on how it goes - want to consider wiring the audio in side of the BOSE amp to the pre-outs on your head unit, if you've got enough.
Oh and you won't be able to replace the BOSE speakers either, as they're 2ohm not the 4ohm that most aftermarket units are so it'd end up too quiet.
If you don't want BOSE it can be a bit of a 'mare!
1999 156 1.8TS Sport Pack 3
2001 166 3.0 V6 24V Super
2003 156 GTA 3.2 V6 24V
2005 156 1.9 JTDM-Jet Sport
2008 159 1.9 JTDM Lusso
1997 GTV 2.0TS Lusso
2001 147 1.6TS Lusso