Never use the wax ring with the plastic funnel. They serve no purpose and frequently cause clogging problems. To be 100% correct, a flange is supposed to set on top of the finished floor. If new vinyl is applied and makes the flange the thickness of of vinyl below the floor level, a regular ring may still be enough or thicker ring can be used. Much lower than that, you should either replace the flange or add an extension ring or rings to the flange.