The whine you are hearing is commonly refered to as "engine noise". There are many potential causes, likewise many potential fixes. It is not uncommon at all, especially in a vehicle that has a factory amplified system. ie. Bose, Harmon Kardon, Infinity. I am going to assume you have factory bose. If thats the case, it maybe a little more difficult to resolve. First we need to know how the unit was installed and integrated into the bose. Chances are they just went speaker level in. Thus running a high level signal into a low level input on the amp. You can try to use a pair of RCAs and cut one end off and hook that to the speaker wires in the vehicle then just plug the other end into the output on the radio. This will run a low level signal to the amp. Also check the ground. This is very important. You need a good ground. Also bad spark plugs can cause engine noise, However I suspect if this was the culprit you would have noticed it with the stock unit.
