How can I allocate GTFS fares depending on the time e.g. off-peak/peak times?
There is no explicit way to handle different fares at different times of day within the context of GTFS. I see several discussions, the most comprehensive of which seems to be this one (which is very old -- as of Nov. 2015, the most recent reply on the thread is from early 2011).
A workaround proposed there is to use multiple route IDs for each route, because fare_rules allows for a fare to be associated with a particular route. For instance, if the route ID was X, the trips that run during the peak might have a different route ID X_peak with a different entry in fare_rules.