Learn Finnish: Kun meri on rauhallinen, aalto on pieni. - When the sea is calm, the wave is small.

Yes! In Finnish, you must always separate a main clause and a subordinate clause (like one starting with kun) with a comma. Since the kun clause comes first here, the comma goes at the end of it, right before the main clause aalto on pieni.

Does starting the sentence with the kun clause change the word order of the second half?

No, it doesn't. Unlike some other European languages, placing a subordinate clause first doesn't flip the verb and subject in the main clause. The main clause stays in its normal order: subject (aalto), then verb (on), then adjective (pieni).

Why are the adjectives rauhallinen and pieni in the basic nominative form instead of the partitive?

Because the subjects they describe (meri and aalto) are singular, countable nouns. If we were describing an uncountable mass noun (like water), we would use the partitive (for example, vesi on kylmää). But a sea and a wave are treated as individual, countable things here.

I sometimes mix up kun and jos. Could we use jos here instead?

You could use jos (if), but it changes the meaning slightly. Kun (when) is used for things that actually happen or general facts, meaning "whenever the sea is calm." Jos is strictly conditional, meaning "in the event that the sea is calm."