Right, you’re seeing multimodality because each sine wave could be the other one. And you’re right that the way to address it is doing something like imposing an ordering via priors. Take a look at the ordered transform, or you could define your priors on say the frequency something like:
freq1 = pm.SomePositiveDistribution("freq1", ...)
delta_freq = pm.SomePositiveDistribution("delta_freq", ...)
freq2 = pm.Deterministic("freq2", freq1 + delta_freq)
to get the same effect. Another way to do it would be with pm.Potential.