Plugins in ...sourcemod/plugins/ folder = load automatically on map change, need unload manually
Plugins in ...sourcemod/plugins/disabled/ folder = need manually load and unload.
You see more server commands with
sm plugins
You can see examples of warmode configs.
<game folder>/cfg/sourcemod/
https://wiki.alliedmods.net/War_Mode_(SourceMod)
*edit
Some plugins have own cvar, to enable/disable plugin.
You may need look plugin config file from
<game folder>/cfg/sourcemod/
And remove that cvar from there.
Then place cvar in map configs. (and/or in server.cfg)
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