Question

When will be the potential energy be negative?

Answer 1

This depends on your reference point. Let us take:

PotentialEnergy=m∗g∗h

In this picture then:

PE1=m∗g∗h

PE2=m∗g∗(−h)

So, in the case of Object 2, the Potential Energy is negative.

Hence, Potential Energy can be negative.Yes, potential energy can be negative.

When you throw a stone up in air, it gains positive potential energy (m g h) considering ground as origin.
Planets being in gravitational field of Sun, have negative potential energy.
Negative potential energy just signifies that the planet is bounded and requires similar energy from outside to get freedom from the gravitational field of Sun.
Same is the case with electrons bounded to atoms in Quantum Physics.