To study the bulk properties of the quark-gluon-plasma (QGP) produced at the beam energy scan (BES) energies at the Relativistic Heavy Ion Collider (RHIC), we extend the (3+1)-dimensional viscous hydrodynamics CLVisc to include net baryon number conservation and Israel-Stewart-like equation for baryon diffusion with the NEOS-BQS equation of state, fluctuating initial conditions from Monte-Carlo Glauber model, and the afterburner SMASH. This integrated framework is shown to provide a good description of identified particle spectra, mean transverse momenta and anisotropic flows for different centralities and over a wide range of collision energies (7.7-62.4 GeV). It is found that the mean momenta of identified particles and anisotropic flows increases mildly with the collision energy due to larger radial flow. We further compute the multiple-particle cumulant ratio $v_2{4}/v_2{2}$ of elliptic flow across BES energies, and find that the relative fluctuations of elliptic flow are insensitive to the collision energy, consistent with the preliminary STAR data. Our model provides a benchmark for understanding the RHIC-BES data and studying the critical properties and phase structure of hot and dense QCD matter.