The callsign shouldn't make any difference to the airport arrival/departure boards - on all the airport systems I have used they take the feed from the commercial flight number. Normally you have several coloums on the airport system - one of which will show the commercial flight number and the another that will show the atc callsign.
The runway slots are applied for using the commercial flight number (which is what shows on the airport system) then the airline publishes a list of ATC callsigns which the handling agent or airfield operations will need to input into the airport system - can be a hassle when the seasons change but once they in they only need to be altered if the callsigns change.
With the airlines I work with it is getting rarer and rarer that the commercial flight number and ATC callsigns match!
Last edited by Mr.Kite; 4th April 2013 at 10:23.