Synaptic scaling is a compensation mechanism that adjusts all synapses by the same relative amount to regulate neuronal activity. However, synaptic compensation does not always scale uniformly, leaving to question if a scaling rule is required to regulate circuit output. We previously showed that scaling up excitatory synapses on motoneurons regulates the respiratory network following inactivity caused by hibernation in frogs (Santin et al., 2017). Although synaptic scaling is thought to involve a scaling factor that multiplicatively upregulates synaptic strength, we find here that distinct mechanisms account for the upregulation of mean synaptic strength and the scaling organization. These processes are separable, as blocking L-type Ca2+ channels undoes the scaling pattern of compensation but does not interfere with the mean increase in synaptic drive. Strikingly, motor output from the respiratory network was weaker when motoneuron synapses were "unscaled" despite having the same average amount of compensation after hibernation. Thus, parallel mechanisms regulate the amount and organizational pattern of synaptic scaling, and both must work appropriately for proper network function. Collectively, these results emphasize that an apparently normal amount of synaptic compensation may still lead to circuit dysfunction in neurological disorders if the balance of synaptic inputs is not accurately regulated.