Yossarian nailed it--you'd only need to cut the terminal ends off the car's speaker wires and extend them, if needed, to reach the replacement speakers. For that, it's better to have a wiring diagram for the model so you get the proper connections. An amp/sub is a bit more involved--I can't remember how I wired mine, but in theory, you'd need a rear 'center speaker' connection as input to the amp. The problem is that the speaker holes are of odd size, so most aftermarket speakers need to use a spacer to adapt the speaker to the hole in the door panel or deck. What this means, if you're using Crutchfield, is to search for speakers based in what vehicle you're installing them into. Not sure if Crutchfield has this option, but I'll look into it.
A second point Y brought up--Bavsound makes the system better, but not outstanding. Back in the 00's, a car magazine called the basic BMW sound system as akin to "the sound of a cheap transistor radio." They were not wrong. Bavsound helps, but if you're up to speed on current stereo components, you could do better. The problem is simply getting a professional speaker system to look like it was factory-installed.
Like Yossarian, I have a convertible, and I hated the original stereo system. I installed BSW speakers and found the audio to be clearer than it was. I installed the amp and sub a couple months later and noticed a real improvement, but in both cases, I needed a higher volume to really get better performance (I kept the original radio). Since I normally listen to music at lower levels, I don't always see an improvement, and I frequently need to correct Bass, Treble, and Fader levels on the radio to get good performance. And stereo performance changes greatly whether the top is up or down, so changing BTF levels is definitely required.
I'm not a stereo pro, and grew up when the 6x9" speaker ruled the world. I don't know the current prices or better manufacturers, so I can't help with that, but if I get out to the car, I can post some of the speaker hole sizes and wiring color codes.