The ATLAS detector at CERN's LHC is preparing to take data from the first proton-proton collisions expected in the next few months. We report on the analysis of simulated data samples for production of heavy Quarqonium states J/ψ→μμ and Υ→μμ, corresponding to an integrated luminosity of 10 pb-1 with center of mass energy of 14 TeV expected at the early ATLAS data. The report will review various aspects of prompt Quarqonium production at LHC: the accessible ranges in transverse momentum and pseudorapidity, spin alignment of vector states, separation of color octet and color singlet production mechanism and feasibility of observing radiative decays of χ c and χ b decays. Strategies of various measurements are outlined and methods of separating promptly produced J/ψ and Υ mesons from various backgrounds are discussed.