We report the study of the skyrmion state near the surface of Cu$_2$OSeO$_3$ using soft resonant elastic x-ray scattering (REXS) at the Cu $L_3$ edge. Within the lateral sampling area of $200 times 200$ $mu$m$^2$, we found a long-range-ordered skyrmion lattice phase as well as the formation of skyrmion domains via the multiple splitting of the diffraction spots. In a recent REXS study of the skyrmion phase of Cu$_2$OSeO$_3$ [Phys. Rev. Lett. 112, 167202 (2014)], Langner et al. reported the observation of the unexpected existence of two distinct skyrmion sublattices that arise from inequivalent Cu sites, and that the rotation and superposition of the two periodic structures leads to a moir{e} pattern. However, we find no energy splitting of the Cu peak in x-ray absorption measurements and, instead, discuss alternative origins of the peak splitting. In particular, we find that for magnetic field directions deviating from the major cubic axes, a multidomain skyrmion lattice state is obtained, which consistently explains the splitting of the magnetic spots into two - and more - peaks.