  Aims: We present and study spatially resolved imaging obtained with the
Atacama Large Millimeter/submillimeter Array (ALMA) of multiple
$^{12}$CO($J=$6$-$5, 8$-$7 and 9$-$8) and two H$_2$O(2$_{02}-$1$_{11}$ and
2$_{11}-$2$_{02}$) emission lines and cold dust continuum toward the
gravitationally lensed dusty star forming galaxy SPT0346-52 at z=$5.656$.
Methods: Using a visibility-domain source-plane reconstruction we probe the
structure and dynamics of the different components of the interstellar medium
(ISM) in this galaxy down to scales of 1 kpc in the source plane. Results:
Measurements of the intrinsic sizes of the different CO emission lines indicate
that the higher J transitions trace more compact regions in the galaxy.
Similarly, we find smaller dust continuum intrinsic sizes with decreasing
wavelength, based on observations at rest-frame 130, 300 and 450$\mu$m. The
source shows significant velocity structure, and clear asymmetry where an
elongated structure is observed in the source plane with significant variations
in their reconstructed sizes. This could be attributed to a compact merger or
turbulent disk rotation. The differences in velocity structure through the
different line tracers, however, hint at the former scenario in agreement with
previous [CII] line imaging results. Measurements of the CO line ratios and
magnifications yield significant variations as a function of velocity,
suggesting that modeling of the ISM using integrated values could be
misinterpreted. Modeling of the ISM in SPT0346-52 based on delensed fluxes
indicate a highly dense and warm medium, qualitatively similar to that observed
in high redshift quasar hosts.
