A pair of superconducting transverse deflecting RF cavities has been studied in the QBA low emittance lattices of 3 GeV TPS for generating ultra short X-ray pulses. Three configurations with different locations for the two cavities in a super-period of the TPS ring are investigated. During numerous turns of the electron tracking, the nonlinear effects between the cavities, the energy spread, the momentum compaction factor, and the synchrotron radiation effects are taken into account. The configuration with positioning the RF deflectors between the QBA cells in each super-period as an optimum arrangement gives rise to better quality electron bunches and radiated photon pulses. The FWHM of the radiated photon pulses of about 540 fs with an acceptable intensity is attained by optimizing the compression optical elements of the TPS photon beam line. Furthermore, the effects of the electron bunch length are studied by alternatively employing an accelerating RF cavity operating with 1.1 MV and 3.0 MV, respectively. The operation of the accelerating RF cavity at 3.0 MV improved the intensity of the photon pulses up to 30% and reduced the equilibrium vertical emittance down to 70 pm-rad. The error tolerance for the deflecting cavities, QBA lattice and injection process are also evaluated.