First of all, I have a 2018 Limited with "premium JBL audio" and honestly think it's pretty nice for a factory sound system. I had a 2016 Limited before, same sound system, equally impressive. But I'm completely replacing it at the moment to a pretty high-end setup, replacing literally everything audio-related.
I'd try going to Crutchfield. For basic to intermediate setups, they'll know what speakers fit your model of car and they'll also know what harnesses are needed to adapt to your car without cutting any factory wiring. They also provide adapter rings between the stock speaker mount points and whatever speakers you choose. They have a pretty wide range of $$$ options for speakers, so you don't have to pay $500/pair (but you can). Although you can pretty much make any speakers fit (with enough fabrication), if you're just wanting to swap speakers, their website will limit you to things that they know will fit your model car and have adapter rings if the bolt patterns or depth of the new speakers aren't the same as the stock ones.
If you're going to keep the factory head unit (the "radio" part in your dash) but run off of a new amplifier, you'd have to go with the line-out converter (LOC) mentioned already. Even then, Crutchfield has all the adapters/harnesses you need to intercept the speaker signals coming out of the stock head unit, redirect to the LOC which converts speaker-level signal to pre-amp level signal for your amp and then take the amp speaker output and send it back into the factory wiring harness.
I'm not sure if you're talking about doing this in a gen5 4runner or something else, but I'm going to assume a 4runner. Anyway, the tweeters and front door speakers are run in parallel (both left in parallel and both right in parallel) and there are consequences when you're running a new amp. If you run speakers in parallel, it drops the "load" (impedance) that that channel of the amplifier "sees" and that channel will get more power than you'd get otherwise when running only one speaker on that amp channel. Unless your amp has sufficient control for all channels, the front speakers will be much louder than the rears and you'd have to fade to the rear to get a better "in your head" sound. One solution is to get "component" speaker pairs that have a tweeter/woofer combo that aren't physically connected. They probably come with a crossover that will limit what frequencies each speaker gets and they're meant to run as a pair in parallel and you can then mount the tweeter in the dash and woofer in the door.
I'm not sure how the rear hatch speakers are wired in. Maybe in parallel with the 2nd row door speakers. I haven't researched it because I'll be replacing them and running them on a devoted channel.
If you're changing the head unit, you don't need the LOC. It will have RCA's (pre-amp level signal) that you run straight to the amp. Then you need more hardware to preserve the functionality that you got with the factory stereo like steering wheel controls, backup camera, etc. But again Crutchfield will know what all you need. I have about 6 bags of harnesses for my upgrade stacked on a pile of boxes of amps, speakers, sound deadening, head unit, cabling, etc.
The short story is to read a lot about this stuff and go from there. I mention Crutchfield, but that's just because they're pretty good about giving you all the bits and pieces you don't realize you need. Maybe there's a better site.