I have a question about adding the Young Template to a Frost Drake from Bestiary 2, when I add it does it also decrease the damage die of the breath weapon by one step? Or is it only for physical attacks?
Good question. I'd say yes, but I'd like to know what others think. What about monsters with spell-like abilities/caster levels? Would these decrease too?
CL is based on hit dice (in some manner). The template does not decrease hit dice, so it will not decrease caster level. Also, no the breath weapon die size does not decrease. Look at the true dragons. The die size does not change as it changes age category, rather it just adds a few extra of the same size dice. A +1 flaming longsword for a handling and for a human do the same amount of fire damage, even though the base weapon changes sizes.
Basically, if the template doesn't say it changes something, it doesn't change. Size changes only alter physical ability scores, reach, space, attack bonus and manufactured/natural weapon damage. If you were to alter the creature the long way, by adding or removing hit dice, then things like CL and the number of breath weapon dice or available abilities would change.
They are called simple templates for a reason. They are meant to be just a quick patch to get something close to what you want without several hours of work rewriting a whole stat block.
CR is not an exact science. Just eyeball it and if the breath seems too potent on a CR 6. drop the DC two points and drop one D6 off the damage.