How do you wire a pair of 6x9 speakers to a 2-channel amp?

What head unit do you have and what amp? Generally, RCA are used for signal interconnections not for speaker outputs if there is anything above a few watts,
Knowing what you have to work with might make it easier.

Depends on the amp and its connections. Some are simple, others can be a mess. The catch with your installation is how the head unit is set up. The amp powering a set of subs and the head unit with the other 4 should be possible depending on the unit. Are you using any of the original parts?

Okay, for that unit if you are using the amp inside the unit, you connect up the 4 other speakers to the circled wires in the harness. So gray and gray black for right front, white and white, black for left front, purple and purple, black for right rear and green and green, black for left rear. (The ones with the black stripe go to the negative terminal on the speakers) Then the subwoofer amp gets fed from the SW RCA jacks. Then you have to use the 2-way crossover setting.

If you are using a different amp for the 4 speakers, then you use the RCA output jacks to connect the LF RF RR LR outputs to the correct line inputs on that amp and still set the head unit for 2-way crossover.
If you are not using the internal amp in the head unit, be sure to isolate the speaker wires and tape them up so they cannot short out on anything.

So, you are thinking 4 door speakers plus 2 6X9 and then 2 subwoofers? Don't think that will work. Many of those style units cut the internal amp when you plug into the secondary outputs. So, if you plug into the "rear" RCA jacks for the XM amp and 6X9s it will turn off the internal amp and you lose the power to the 4 other speakers. The info doesn't say so, but many do that. You should be able to tell if you connect up just the 4 door speakers first, test that it works. Now plug in the subwoofers and see if they work. If you get 4 door speakers and subwoofer then for testing unplug the subwoofer and plug it into the rear speaker RCA connectors, do you still have all 4 door speakers? If not, then it does mute the output and limits you to just the 4 door speakers and the subwoofers.

Different head unit would likely still work the same way. What you normally do is determine how many pairs of speakers you want and then use one amp per pair. But extra speakers really doesn't improve the sound unless you have a large area and a way to tune the speakers to match the interior of the vehicle acoustically. The large speaker count in modern vehicles are due to them adding individual woofers, midrange and tweeters to create better sound to tune them to match the vehicle. The issue with splitters is that you can create problems if the units you are feeding the signals into are not perfectly matched in all ways. You get what is known as ground loop interference because they are not evenly matched. The result is hum or strange acoustic feedback.

Ground loop isolator might help but may not eliminate the problem. Usually the amps don't require a lot of power to turn them on if they have remote sense. If they don't you can use the remote wire (blue with white) to trigger a relay to turn them on and off.