Mass flow rate inlet boundary condition allows for specification of mass flow rate. Here, the total pressure is not fixed and will rise to whatever value is necessary based on the computed static pressure. This value of static pressure is dependent on the mass flow rate specified. In the boundary condition panel. The static pressure (you specified) will be used only when your flow is supersonic or if you are initializing the solution from your mass flow inlet boundary condition. This value will be ignored if your flow is subsonic.
Static pressure is always specified relative to the operating pressure. Unless you make a change, operating pressure is always set to 1 atm. Negative values of static pressure, if your operating conditions are set to 1 atm, are not an issue. It just means that your absolute pressure is lower than 1 atm.
Please have a look at sections 6.3.5 - Mass-flow inlet boundary conditions, 188.8.131.52.7 - defining static pressure, and 7.14.1 The significance of operating pressure from the Fluent Users Guide. This will provide you with a better understanding.
I hope this helps.