The period of stay in Turkey provided by the visa or visa exemption cannot exceed ninety days within a period of one hundred and eighty days. In case that foreigners, who have stayed in Turkey ninety days within a period of one hundred and eighty days, come to Turkey again; unless there is another matter preventing them from entering into Turkey at the border gates, they are required to enter into Turkey by filling the ‘Residence Permit Conditional Entry Information Form’ and apply for residence permit to the Governorate of the city they reside within ten (10) days as of the date of entry.
System is simple, when you come to Turkey, police computer system automatickly counts the days you stayed in Turkey in last 180 days and if less than 90 days system lets you enter the country.
If it is 89 days you can enter to leave the country same day. System counts the the day you entered as one day and the day you leaved as one day. If you enter at 23.59 you lost one day for just one minute.
For example, you are at the border to enter, Today 1st of December system will start counting the days you stayed from 4th of June. (some months 31 days)
Another example, If you want to come to Turkey every month for 14 days you will not have any probs becouse you will not complete 90 days in 180 days. You will just need to renew your e-visa when expires.