I've always found this description of the setup in the manual a helpful one:

Operation and Setup
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To operate your CSP3, install the tubes, hook up the output jacks to the amplifier. Once you are sure the amplifier and preamp are securely connected together with a high quality interconnect cable between 1 and 5 meters in length you may plug both units into the wall outlet.
Before you turn either piece on make sure that all of the controls on the CSP3 are turned all the way down.
Turn on the CSP3 and let it warm up for one minute. Double check that all the controls are down all the way, including the volume and that the interconnect cables are securely installed into the output jacks of the CSP3 and the input jacks of your amplifier.
Turn on the amplifier. The amplifier should come on and if has a gain control on it, turn it up to the half way point. Your system is now on and at idle. Any noise or hum that you hear is your system reference. Make a note of it so that later when we connect our sources we can see if they added any noise or hum.
It is now time to connect your first source component to one of the input pairs on the CSP3. You can do this while the CSP3 and your amplifier are on and at idle, but be sure you haven’t turned any of the controls on the CSP3 up yet.
If you didn’t hear any hum or noise increase when you connected your first source that means that A) your cables are probably good and B) there is no ground loop between the components.
No add your second source if you have one and again listen for any increase in noise or hum. If with either source you DO notice an increase in noise or hum then it comes from cables or small ground loops between the components or both. The key here: is the noise or hum acceptable? For example if you have to put your face up to the loudspeaker to hear it, it’s acceptable. If however you can hear it from the listening chair it is not acceptable and should be corrected before going any further.
Once everything is connected and warmed up and you are happy that there are no excessive amounts of noise or hum, you can set the controls on the CSP3 to match your amplifier’s requirements:
1) turn up the input level controls all the way (clockwise). These are only adjusted during headphone use and only with headphones that get too loud.
2) turn on your source and get some music playing.
3) turn up the main volume control on the CSP3 to halfway.
4) slowly turn the output level controls up until you hear
music playing at a normal listening volume.
5) your preamp is now adjusted properly for your amplifier.
6) further experimentation can be made by adjusting the gain control on the amplifier if it has one relative to the output level settings on the CSP3.

I have used it both ways. Currently I have it before the CSP3 so that headphone listening benefits.

The two pots closest to the front are the Input pots.

Odds are you might have the best sound this way. According to the manual Steve does indicate that the input pots are for headphones and says leave them be if notusing those. (I never leave anything be though, in my other system and wtih a CSP2+ with the mods I have them on 7 or 8). In my CSP3 with the 25th Anniversary mods Steve bypassed the input pots and gave me a glass resistor. So I can only adjust the output pots. Using a ZTPRE, ZBIT and ZROCK2 before the CSP3 my output pots are generally low, 4 or 5.

I haven't used my Torii III in a few months but when I used it with the CSP2+ preamp I'm pretty sure I never had the Torii volume pot above half way unless it was party mode and clarity wasn't a concern.

JD

Playing with the Inputs vs the Outputs I honestly don't hear a difference.  For all I know, they are wired the same.

I currently have 6N1P-EVs in all three positions.  I used to run a Tungsram PCC88 in the front slot but I had 2 go bad prematurely  (never when used in my ZMA though).

I need to play around more.  Last night I was only playing some Mozart symphonies and they may not have been the best music to notice changes.