We have obtained three-dimensional maps of the universe in $\sim200\times200\times80$ comoving Mpc$^3$ (cMpc$^3$) volumes each at $z=5.7$ and $6.6$ based on a spectroscopic sample of 179 galaxies that achieves $\gtrsim80$\% completeness down to the Ly$\alpha$ luminosity of $\log(L_{\rm Ly\alpha}/[\mathrm{erg\ s^{-1}}])=43.0$, based on our Keck and Gemini observations and the literature. The maps reveal filamentary large-scale structures and two remarkable overdensities made out of at least 44 and 12 galaxies at $z=5.692$ (z57OD) and $z=6.585$ (z66OD), respectively, making z66OD the most distant overdensity spectroscopically confirmed to date with $>10$ spectroscopically confirmed galaxies. We compare spatial distributions of submillimeter galaxies at $z\simeq 4-6$ with our $z=5.7$ galaxies forming the large-scale structures, and detect a $99.97\%$ signal of cross correlation, indicative of a clear coincidence of dusty star-forming galaxy and dust unobscured galaxy formation at this early epoch. The galaxies in z57OD and z66OD are actively forming stars with star formation rates (SFRs) $\gtrsim5$ times higher than the main sequence, and particularly the SFR density in z57OD is 10 times higher than the cosmic average at the redshift (a.k.a. the Madau-Lilly plot). Comparisons with numerical simulations suggest that z57OD and z66OD are protoclusters that are progenitors of the present-day clusters with halo masses of $\sim10^{14}\ \mathrm{M_\odot}$.