Transitioning from F-1 to H-1B Without Curricular Practical Training

Hi,

I am currently in US in F-1 status and I have two approved H1B petitions.
I have not worked in OPT and will be in school till 30th September.
I will be joining my employer on 5th October.
I have following questions.
What would be the best time to notify the DSO at my school, towards the end of September or should I notify them earlier?
Can it somehow affect my change of status petition?

You can inform your DSO at any time you choose. There's no reason to delay and, generally speaking, earlier is better.