There is no such thing as 'negative energy'. Energy is a description of potential state changes within a system. A system cannot not change in a manner less than if it does nothing!
You may freely define a quantity of 'potential' which may be negative with respect to some other vaule or system. In the case of an atom, the 'ground state' is the state where everything is settled and huncky-dory (that is, nothing is likely to spontaneously change) with all the electrons in their 'rightful place'. It requires energy to pull that electron off the hydrogen atom, leaving behind a 'potential hole' into which an electron will get sucked at the first opportunity so that it can get back to 'ground state'. Therefore it is denoted -ve indicating whether a return to the ground state will require, or release, energy in doing so.
Naturally, your definitions can be your own - if you were to want to define all reactions as 'a release of energy', then those that are endothermic and need energy would be a 'negative energy' process. So it is all in your definition, but the accepted convention is that a +ve ionised atom will carry a 'negative potential'.