Hi, my 97 SSE has a great bose factory system but I want to install a Blaupunkt SD27 head unit. Will the bose amp work or do i need to change everything?

Everything will work, just get the correct wire harness for your head unit/car. I don't think there'* anything to change(don't remember doing anything when I changed).

It'* hard to find the correct harness (With the adapter for the bose amp power). If you aren't afraid of doing a little re-wiring and have the tools handy (Several butt connectors, a wire stripper/crimper, and preferably a pair of scissors and some electrical tape), you can do it yourself. The only additional steps you need to perform are to cut the amp power line out of the harness (leave a few inches on the harness in case you ever want to go back to stock, it'* a pain to rewire for it to work again... trust me.) Once you have cut the amp line out, wire it into either end of the accessory power line (usually red or orange-red).