I am a 6th level priest who can cast animate dead. For this purpose let's assume I always cast Desecrate before creating undead.
My base limit is 12HD but if created in the effect of desecrate the limit it doubled to 24 HD.
As I understand it, the total max I can control is 12HD despite being able to create up to a 24HD undead in a single casting using desecrate.
I have the capacity to create a Bloody Hill Giant Skeleton(10HD base, x2 with the Bloody Template)but I could not control a second Bloody Hill Giant Skeleton because that woudl exceed my 12 HD control limit.
The max you can control is 4 times your CL. 24.
The max amount of HD you can animate with a single casting of Animate Dead is equal to your CL, 6. Casting Desecrate doubles this to 12.
Templated undead count against your single cast HD limit, not your maximum capacity for controlling. You would need to be able to animate 20 HD worth of undead with a single casting in order to animate a bloody hill giant skeleton. But once you manage to do it, the skeleton will only use up 10 HD of your maximum capacity.