I'm one of those who loves a GREAT sounding car stereo (nothing replaces the sound of a well-running hot rod, though).
Currently, I have a Retrosound Model 2 with Retrosound 4x6s in the doors, and 6x9s in the package tray of my '71. The interior is completely deadened with RAAMat, which helps the stereo work more efficiently (without having to compete with unwanted noises that would otherwise soak-in through vibrations and empty spaces). The system is merely 'adequate,' IMHO. Its sound is roughly along the same lines as a nice 4-speaker set-up in a '90s to mid-2000s car: not quite all there, kind of flat, and not a lot of power.
To help it along, I have a set of MTX Terminator 10" subs with a matching MTX Terminator 200 watt amp... which, now I just need to get off me arse and build the box to fit behind the rear seat (non-fold down). Once that's finally in, I'll tune it to what I call a 'generic' setting - that's where the bass output level is somewhere in the middle of the amp's powerband in relation to the rest of the sound output from the other speakers - and I set the head unit's crossover to block anything below 120Hz from going to the main speakers and send everything below 120Hz to the subs (to kill off any chance of bass distortion through the main speakers). From that point, if one of the tunes isn't putting out enough bass for my liking, I can turn up the amp's 'gain' a little to get the full sound I want... and turn it back down for other tunes that have too much. That's really the only way to get at least close to what you want without having to constantly mess with the EQ or Bass/Mid/High settings buried way down deep in the stereo's menu of options (no more simple knobs or buttons to handle single functions like that anymore on modern stereos, after all). I'd be surprised if I'm pushing the amp and subs past 40% of their capabilities, even when I have it all cranked up while on my way to work.
I've had similar set-ups in my trucks/daily drivers: Decent lower/mid-range aftermarket head unit, factory or mid-range aftermarket speakers, and a nice set of mid-range subs with about 200watts of amp. I like nice full sound with a confident bass presence - it's gotta be there. Now, I'm not saying I'm into the boomy stuff or anything like that, but I do have a few tunes that can get like that and it's gotta be done right when it does. Most of my other daily driver systems have been JVC head unit, Infinity speakers, and MTX subs, but I've had good luck with Pioneer and Kenwood head units as well as Kicker subs.
Just because you're adding an amp and subs to round out your system, doesn't mean you need to tune it to keep up with hood rats and their rolling bass cannons.
Hope this helps!