Was the vehicle retitled in the name of the S Corp?  I'll assume not.  In which case, I would probably just use standard mileage rate.  Then have the S Corp reimburse at SMR for 10/1 - 12/31/17 to catch up and for 2018+.

If the vehicle was contributed to the S Corp and retitled then you'll probably need to override depreciation and manually split the year between Sch C and the 1120S.

Rick