The (Li$_{1-x}$Fe$_{x}$OH)FeSe superconductor has been suspected to exhibit long-range magnetic ordering due to Fe substitution in the LiOH layer. However, no direct observation such as magnetic reflection from neutron diffraction has be reported. Here, we use a chemical design strategy to manipulate the doping level of transition metals in the LiOH layer to tune the magnetic properties of the (Li$_{1-x-y}$Fe$_{x}$Mn$_{y}$OD)FeSe system. We find Mn doping exclusively replaces Li in the hydroxide layer resulting in enhanced magnetization in the (Li$_{0.876}$Fe$_{0.062}$Mn$_{0.062}$OD)FeSe superconductor without significantly altering the superconducting behavior as resolved by magnetic susceptibility and electrical/thermal transport measurements. As a result, long-range magnetic ordering was observed below 12 K with neutron diffraction measurements. This work has implications for the design of magnetic superconductors for the fundamental understanding of superconductivity and magnetism in the iron chalcogenide system as well as exploitation as functional materials for next generation devices.