Why do we put "is" before "your" but not "Not only your son is....."?
There are a number of situations where the verb (e.g.'is') is placed before the subject (e.g. 'your son'). This is called inversion. One of these situations is in expressions starting with 'only' or 'not only'. You will notice that following these any subject/verb pairs are not inverted.
Only after the meeting did I
realize the importance of the subject.
Only after the rain had started did he
realise he had
Not only is the cup
empty, it is
There are plenty of web resources about inversion, and it is a topic in many grammar books. Here is just one of many sites where you can see some other times when it is used:
A Google search e.g. for "English grammar verb inversion' will find you plenty of others.