If you are only slightly sore, exercise can bring relief. You can do light resistance training, core stabilization exercises or low intensity cardio like walking. You can also work on muscles other than the sore muscles (i.e. if the legs are sore, focus on the upper body).
Functional training programs should be designed to allow muscle recovery, which usually takes between 48-72 hours, depending no the type and intensity of training. For heavy lifting, you can work different muscle groups on different days. Large muscle groups (quads and hamstrings) should be given greater amount of time to recover (i.e. 72 hours), while smaller muscles like the core are built for endurance and therefore can be worked more frequently (i.e. every 48 hours).