If i was to install a aftermarket stero head unit would it work with the Bose speakers....

only if you can hook it up so the HU doesn't
 

try to amplify the speakers. They already have amplifiers, so they'd blow.

is this something people do with good results? I like the way the Bose sounds. My HU has just seen
 

better days, plus i would love to have a cd player as opposed to my alpine 6 cd changer....

You could run wires directly to the speakers and bypass the bose amplifiers

if HU have line-outs then of course yes
 

the second thing to worry about is your HU
disconecting line-outs during track/disc skip
or when searching for stations on the radio
(some HUs do this, some don't)

you may hear a very loud pop during these operations

it can be aliminated almost completely by
separating HU and BOSE amplifiers with
small capacitors (polarity is important here)

all you have to do is solder a little ;)

not unless you replace the bose speakers

Speaking of head units, what dash kit do you guys use?