csgo use server.cfg like other games.
It just launch later those
gamemode_*.cfg files.
And csgo server also try execute
gamemode_*_server.cfg file to override "default" game mode settings. Cvars!!
So use normally server.cfg like before,
and if specific in-game cvar not stay to wanted value when map change, it maybe locate in gamemode_*.cfg,
to override, use gamemode_*_server.cfg
*edit
To be MORE clarify. Add in gamemode_*_server.cfg file only cvars what are in gamemode_*.cfg. Nothing else and it stay more clear
*and don't edit gamemode_*.cfg, it will be overwritten back when you update your server via SteamCMD