If you are using the menu system, press the key you have bound to ‘admin’
Select ‘8 Plug-in Config’
Select an plug-in configuration option you wish to toggle.
Note that by changing these options it will be permanent unless the associated server var (e.g. mani_adverts) is in the server.cfg file.
This is not particularly comprehensive at the moment but is enough to enable/disable major functionality.
The mani plugin server vars can also be changed by using adminrcon or using normal rcon.