To the OP here is an excellent link detailing some common problems with BOSE speakers:
http://www.intellexual.net/bose.html
If you have the option to return them, you would definitely be happier with independant components rather than an all-in-one type system.
If you don't have the option in returning them, some simple splicing and some new cable would provide a more pleasing look to the cables. Also if you have carpet, tucking the cabling between the baseboard and the carpet is a very effective way of hiding any unsightly cable. That requires nothing more than some patience and a butter knife.
There are a lot of misconceptions about speaker cable making a difference in audio quality. The only thing you need to look for in speaker cable is making sure you have the correct AWG for your distances.