Unless you are very good at integration you won't be able to use the Bose system, complete or otherwise, in your SE. I would instead replace all your speakers first as a starting point. I agree that Pioneer offers the best bang for the buck, but more expensive does not necessarily mean better.
Since you are keeping your factory head unit (stereo), I would shoot for replacement speakers that have a low RMS rating (The higher the rating, the more power that is required to drive them).
Also keep in mind GM factory stereos, more often the newer (94-99 I know at least), have an inverse proportional bass response. In normal speak: the higher you turn the volume up, the more the bass "flattens" in an attempt to save the speakers from killing themselves (provided those speakers are factory). Even the factory stereos with the EQ in them do this.
Welcome, downwardly mobile yuppies, to the dawn of the Age of Nefarious.
1993 SSEi - FrankenJinx - dead and gone.
1994 SSE (136K strong) - 180* t-stat,HD alternator, most unequipped SSE on the club, XM radio, Kenwood CD/MP3.
2006 Chevy Malibu Maxx LTZ - Custom 2.25" manifold-back exhaust w/FM-80. Probably the only Maxx with this system.