One thing to consider is whether your amp is designed to take single ended or differential (aka balanced) inputs. All higher quality (which Bose claims to be) car audio uses balanced signalling (one cable carries positive signal swing and the other the exact same but negative) this reduces the noise tremendously.
Now, if it is balanced and you are feeding it single ended signal (one wire is signal the other ground), which all cheap sound cards are you will introduce ALOT of noise into the system which the amp will be unable to cope with.
If you determine that this is the case you will have to convert your single ended signal to balanced one, there are several options and I've tried most of them
... I can post more details if you are interested.
Mark