A variant channeling either modifies positive channeled energy when used to heal or modifies negative energy when used to harm.
So, only the heal bonus. No harm bonus from channeling positive energy. As a result, the Undeath variant is a difficult FAQ candidate.
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By RAW, you only gain the heal bonus when channeling positive energy to heal living beings, and only gain the harm bonus when channeling negative energy to harm. Positive energy harming gains no modifier, and negative energy healing gains no modifier.
However, the original author's intent (expressed in a post I cannot find right now) was that all healing (positive or negative) would gain the heal bonus and all harming (positive or negative) would gain the harm bonus. If any of my players choose to take a variant channel, that is how we intend to play it.
EDIT: Found it.
I was just going by this part of the book:
"A variant channeling either modifies positive energy when used to heal or modifies negative energy when used to harm." at the beginning of the third paragraph in the variant channeling section. It doesn't seem to contradict that later anywhere...
I think Undeath might be a special case, it mentions that undead get the 'enhanced' heal effect, which is described at the beginning of the section as well.If I am wrong, hopefully a Paizo employee will point it out, but that seems to be the way it works.
I would certainly prefer having the option of doing either with only positive or only negative. :)
When I wrote that section, I worded it specifically as "heal" and "harm" in order to make it usable with both kinds of energy use (positive as heal (living) or harm (undead) or negative (reversed)).
That was *my* RAI as the writer.
HOWEVER, all Paizo stuff goes through editing and development, and their call is final on all rules elements. My read of the above-referenced sentence in the section is that they chose to make it positive/heal and negative/harm ONLY. That appears to be the RAW, and the RAI of the editing/dev team.
As to the OP's question about the phylactery, because the phylactery has a very specific effect - adding +2d6 to your pos/neg channels - that effect derives from the item and not from your own abilities. While its effect is similar to the 3.0/3.5 item that gave you "turn undead as 4 levels higher," that is not how the PF item works.
The +2d6 is applied AFTER any modifications to your own dice of healing or harming.