[b]First one solution:[/b]
(Example for csgo, but all the same is for css)

[LIST=1]
[*] Edit your cfg\gungame\csgo\gungame.config.txt, set "Enabled" "0"
[*] Copy your cfg\gungame folder into cfg\gungame-disabled
[*] Copy your cfg\gungame folder into cfg\gungame-enabled
[*] Edit your cfg\gungame-enabled\csgo\gungame.config.txt, set "Enabled" "1"
[*] Dont use map/prefix specific configs from cfg/gungame/csgo/maps for enabling gungame
[*] Dont use map/prefix specific configs from maps/cfg for enabling gungame
[*] Download and install MapConfigs plugin from [url=http://forums.alliedmods.net/showpost.php?p=1961467&postcount=85]here[/url]
[*] Create some map/prefix specific configs in cfg\sourcemod\map-cfg for enabling gungame and other plugins
[*] For example create cfg\sourcemod\map-cfg\gg_.cfg
[*] Edit cfg\sourcemod\map-cfg\gg_.cfg and add "sm_gg_cfgdirname gungame-enabled" (without quotes) in it
[*] Edit your cfg\server.cfg and add "sm_gg_cfgdirname gungame-disabled" (without quotes) in it
[/LIST]

[b]Second one solution:[/b]

[quote=BDeep;1009714]I am really lost on this i guess. Lets just say for example that I dont use a plugin to excute configs. How EXACTLY do I do this with just gungame. WOuld I have to make a gg_config for all GG maps and all the other maps that I have? If so thats not really a very good setup becuase I have 100's of maps that would take forever.

Now lets say that I have a plugin that executes a config if a map starts with gg_ and a different config if the map starts with cs_ or de_. If I use this plugin then the buyzones are still gone on cs_ and de_ maps.

The plugin that I was using is my own and can be seen here

What would be nice is if there was simply a cvar in gungame that could be used in a config for turning on and off the buyzone code in your gungame plugin.[/quote]

ok, let's start it from the begining
As i understand your server is running not in gungame-24x7 mode, and gungame should run only on gungame maps, and on other maps it should not be enabled at all. And you have many maps for gungame and many maps for regular game.
First of all you should disable gungame in your cfg/gungame/gungame.config.txt (Enabled "0")
Than you should create particular prefix configs, for example
for gg_* maps you can use prefix "gg" and create config
cfg/gungame/maps/gg.config.txt
or for particular map you should create config with that map name, for example if map is aim_ag_texture, than config will be
cfg/gungame/maps/aim_ag_texture.config.txt
And in that particular configs you should enable gungame
[code]
"GunGame.Config"
{
    "Config"
    {
        "Enabled" "1"
    }
}
[/code]