My business was a C corporation from Jan 2016 to Aug 15,2016 and converted to S corporation that date, do I need to file separate returns?

This is not a simple task and if you are not well versed in the steps you really need to use a professional to get the conversion handled correctly.   https://www.irs.gov/businesses/corporations/filing-requirements-for-filing-status-change-revised-11-...

I agree, go to a tax professional.

Your tax return for the C-corporation was due last week (December 15th), so it it owes anything, there will be late penalties and interest.