The Sage familiar gains two additional skill points per level
A Sage familiar archetype replaces the ability to share the master's skill ranks, which replaces the following ability granted to familiars:
Skills: For each skill in which either the master or the familiar has ranks, use either the normal skill ranks for an animal of that type or the master’s skill ranks, whichever is better. In either case, the familiar uses its own ability modifiers. Regardless of a familiar’s total skill modifiers, some skills may remain beyond the familiar’s ability to use. Familiars treat Acrobatics, Climb, Fly, Perception, Stealth, and Swim as class skills.
Also, note that a normal familiar do not gain any skill ranks to improve their skills, as noted by the following line:
use either the normal skill ranks for an animal of that type
This means that a normal Fox familiar would have the following skills:
Skills Acrobatics +2 (+10 when jumping), Perception +8, Stealth +10, Survival +1 (+5 scent tracking); Racial Modifiers +4 Acrobatics when jumping, +4 Survival when tracking by scent
If we break down the skills to figure out the skill ranks invested on each skill, we have the following:
- Acrobatics: 0 (+2 from dex, this is only listed because of the jumping bonus)
- Perception: 1 (+3 class-skill, +3 skill-focus, +1 perception)
- Stealth: 0 (+2 dex, +8 small-sized)
- Survival: 0 (+1 wis, +4 scent)
That matches the description for skill ranks gained by animals (1 per HD).
A Sage fox familiar, instead of having a single rank in Perception, would gain 3 skill ranks per level of the master to distribute among her skills, and no longer would be able to use her master skill ranks as her own.