Putting more holes in your car just makes things worse. If possible, re-use the holes already there.
A good set of mid (6inch) will produce good base. But if you are going to fill those spots in the back...put in some 6x9's. They are the best bang for the buck usually.
Sound is price. If you want good sounds, you gotta pay the price. Cheap speakers will produce cheap sounds. It doesnt matter if you buy a cheap set of components or a cheap set of 6X9's, they will still produce the same quality of sound.
You can buy a set of MBQuart Components or a pair of Infinity 6X9's that will blow away a low line set of subs, 6x9's, and components. Thus, I recommend that you buy one set of good speakers ie. infinity, pioneer, mbquart, keenwood or some other big name speaker co. You have a pretty small vehicle. You could very easily get away with having a good pair of 6x9's or components. To prevent cutting holes...get some 6x9s or 4x6s if you cant fit them in the hole in the back.