We obtained spectra of the pre-main-sequence star AU Microscopii during a transit of its Neptune-sized planet to investigate its orbit and atmosphere. We used the high-dispersion near-infrared spectrograph InfraRed Doppler (IRD) on the Subaru telescope to detect the Doppler "shadow" from the planet and constrain the projected stellar obliquity. Modeling of the observed planetary Doppler shadow suggests a spin-orbit alignment of the system ( $\lambda =-{4.7}_{-6.4}^{+6.8}$ deg), but additional observations are needed to confirm this finding. We use both the IRD data and spectra obtained with NIRSPEC on Keck II to search for absorption in the 1083 nm line of metastable triplet He I by the planet's atmosphere and place an upper limit for the equivalent width of 3.7 mÅ at 99% confidence. With this limit and a Parker wind model we constrain the escape rate from the atmosphere to $\lt 0.15\mbox{--}0.45$ M⊕ Gyr-1, comparable to the rates predicted by an X-ray and ultraviolet energy-limited escape calculation and hydrodynamic models, but refinement of the planet mass is needed for rigorous tests. * Based on data collected at Subaru Telescope, which is operated by the National Astronomical Observatory of Japan, and the W. M. Keck Observatory, which is supported by the W. M. Keck Foundation and operated by the California Institute of Technology, the University of California and the National Aeronautics and Space Administration.