Using Bernoulli's theorem :
P+ρgh+12ρv2= constant
where P is the absolute pressure at a point, ρ is the density of the fluid, h is the height of that point above a reference point and v is the velocity of fluid at that point.
Thus P1+ρgh1+12ρv21= P2+ρgh2+12ρv22
Subtracting atmospheric pressure from both sides.
We get P1−Po+ρgh1+12ρv21= P2−Po+ρgh2+12ρv22
Gauge pressure P′i=Pi−Po (i=1,2)
⟹ P′1+ρgh1+12ρv21= P′2+ρgh2+12ρv22
Thus the Bernoulli's equation remains in the same form.
Hence, it does not matter if one uses gauge instead of absolute pressure in applying Bernoulli's equation.