The Fe/Gd multilayer system hosts a number of magnetic phases, such as stripe, mixed stripe and skyrmion, skyrmion lattice, and isolated skyrmions for a wide range of temperature and magnetic field. We report different Hall transport signals in a Fe/Gd system through multimodal correlative resonant soft x-ray scattering (RSXS), Hall effect, magneto-optic Kerr effect, and transmission x-ray microscopy measurements. The simultaneous nature of the RSXS and Hall transport measurements allowed us to accurately connect various features in the transport data with the specific magnetic phases. We found that the topological Hall effect (THE) shows peaks with opposite signs, which we attribute to two different mechanisms. Our multimodal correlative study indicates that the sign reversal in THE occurs when the system transforms to and from a skyrmion lattice and low density isolated skyrmion phases. We propose that the skyrmion lattice contributes to the THE through a Berry phase induced emergent magnetic field mechanism in one case, and a skew scattering mechanism corresponding to the isolated low density skyrmion state.