how do templates interact with the amount of hd one can control for undead
They don't. All that matters is HD unless the template had HD. There are no "virtual hd".
I suppose more detail is needed.
If the question is, for example "Can I cast animate dead on the corpse of an Advanced animal to get an Advanced Skeleton or Zombie version out of it?"
that might be different than
"Can I cast animate dead on a dead animal and choose to apply the Advanced template?"
Then "what about Create Undead or i]Create Greater Undead[/i]?"
I think the details may matter based on which scenario.
The spells animate dead, create undead, and create greater undead account for methods by which spellcasters can create a wide range of undead creatures—but the options granted by these spells are limited. With the GM’s permission, these can be adjusted to allow for the creation of additional types of undead. Doing so requires additional material components and spells (additional spells are cast as part of the casting time of the undead creation spell, but do not extend that spell’s casting time).Note that some undead can never be created by create undead or create greater undead. The methods by which these undead can be created are given in their specific monster write-ups. In the Pathfinder RPG Bestiary and Bestiary 2, such undead include the following: ghost, lich, nightshade (all), poltergeist, ravener, revenant, skaveling, vampire, void zombie, and winterwight.
The following table summarizes what spells, minimum caster levels, and additional material components are needed to create other undead with animate dead, create undead, or create greater undead.
The table accompanying that bit of text does not include any additional templates beyond the monsters themselves.
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was thinking more about would juju zombie, or bloody skeleton make it so it takes more hd to control
Numerous variant skeletons exist, such as those whose bones burn with an unending fire and those who drip with gore and reassemble themselves over time. Both of these variant skeletons can be created using animate dead, but they count as twice their normal number of Hit Dice per casting. Once controlled, they count normally against the controller's limit.
Note that juju zombies are separate type of undead, not a template applied to zombies. The naming could have been more clear.
Sorry, to be more clear, juju is a template, but not a variant of the zombie created by animate dead. I was referring to things like bloody skeletons or fast zombies being templates applied to the base undead, which is also not quite accurate, but draws the distinction between juju and the others.
So annoyingly, juju zombie not listed as an option on any undead creation spell on the prd. d20pfsrd lists it under create undead, with no citation on where this option comes from. And the bestiary entry sheds no light, so yeah, how does one make em?
Juju Zombies are among the creatures listed in Undead Revisited. There, it indicates Create Undead is used. The Caster Level required is at least 11th level, and must also be higher than GD of the Undead to be created. In addition, either enervation or energy drain is required as part of the process.
Danged typos... that's "higher than the HD".
Sorry.
So an 11th level caster can make a Juju Zombie of 10 HD or less.
Juju zombie and skeleton champion are nice if you can get bodies with good class levels, some good knowledfe history or nobility checks might point you to good tombs to rob.
The list in Undead Revisited covers up to what was in the Bestiaries at the time (Bestiary 3, I think).
The Advanced Bestiary (from Green Ronin, updated for Pathfinder recently) has a number of "Dread" versions of other undead (Dread Wraith, Dread Zombie, etc.). It also includes template-like directions for creating "standard" versions of the same undead (in some cases). How these would fit with PC spellcasters is not described.