You have to put them in maps/mp/gametypes.
then you've to call the script from the game type you want. for example, if you want to use somescript.gsc and your server has TDM gametype, then you have to open TDM.gsc and add a line after main, just like this:

Code:
/*	Team Deathmatch */
main()
{
......

		level.callbackStartGameType = maps\pam\tdm::Callback_StartGameType;
		level.callbackPlayerConnect = maps\pam\tdm::Callback_PlayerConnect;
		level.callbackPlayerDisconnect = maps\pam\tdm::Callback_PlayerDisconnect;
		level.callbackPlayerDamage = maps\pam\tdm::Callback_PlayerDamage;
		level.callbackPlayerKilled = maps\pam\tdm::Callback_PlayerKilled;
		maps\mp\gametypes\_callbacksetup::SetupCallbacks();
                maps\mp\gametypes\scriptname::Init();

If you face any problems, I can do it manually for you through TeamViewer.