So where should the tubes be?

Never talk a man out of a tube phono stage. Especially not when Decware and Bottlehead make such excellent and reasonably priced tube phono stages.  

Yogiboy is right about they just sound right. I was at a show one time, the same system was being used to demo different tables, platters, and phono stages. They all sounded different but they all sounded great until one, it had this uncomfortable edge to it. Wasn't sure at first but after a couple minutes I turned to Chris and said what is this solid state? Yeah not completely but yeah not all tube.   

So there you go. Use tubes wherever you want music.

Preamp or phono stage.

Where tubes make the biggest impact on the sound is the amplifier.  But, good tube amplifiers also represent the highest cost in making a switch (good output transformers are particularly expensive and important to the sound), so that might not be where one would start.  Also, the matching of a tube amplifier to the speaker is critically important, so you will need to either have some experience or some help in that area (e.g., a good dealer).

I can’t speak for anyone else, but for me:
in the past.

I have an all tube system now—preamplifier, phono preamp, DAC, and amp.  It sounds super. 
Only downside is diagnosing where the “bad tube” is when it happens. It’s 25 total tubes!  Better than it has been here but still lots of tubes to roll and monitor!