This question comes up a lot, and there is no good answer. FTM is not explicitly designed to handle historical locations, so the best advice you'll get here is how people work around this shortcoming in the program.
(As far as I know, at this time none of the other major genealogical programs relate historical locations to modern ones.)
As far as I gather from previous discussions, there are three methods most widely used:
1) Historical place names are used in the place field and the errors from the Place Name Authority (PNA) are ignored; some people go to the extra length of setting the GPS coordinates on the map in the Places workspace, but this data doesn't export and won't even appear in a report, so it's only good for your map screen (it also doesn't translate to the map at ancestry.com for linked trees). People who use this method usually make note of the modern location either in the description (not exportable via GEDCOM) or in the fact notes (exportable, but not visible at ancestry.com for linked trees) or they put it in both. This method is probably the one preferred by the more serious genealogists, because it's true to the data.
2) Modern locations are always used in the place field and note is made of the historical location in the description, notes, or both. This method is probably most compatible with the way FTM and Ancestry.com are set up.
3) Each fact is duplicated so that there are two instances of the place field. In one the modern place is inserted; in the other, the historical.