In this paper we study generalized J-inner matrix valued functions which appear as resolvent matrices in various indefinite interpolation problems. Reproducing kernel indefinite inner product spaces associated with a generalized J-inner matrix valued function W are studied and intensively used in the description of the range of the linear fractional transformation associated with W and applied to the Schur class. For a subclass of generalized J-inner matrix valued function W the notion of associated pair is introduced and factorization formulas for W are found.