The GeoSystems Monitor offers a number of ways in which you can avoid unnecessary alerts from occurring during monitor server application / services maintenance operations. 

The first of these is, of course, by configuring Exclusions for regular scheduled maintenance.  The second is to turn off and on a monitor server from the dashboard.   The third is to either make individual monitoring points active / inactive or turn alerting off or turning all alerts off in the settings.

During initial configuration, you can avoid unnecessary alerts, by setting Alter to No, configuring the monitoring point , making it active and then checking dashboard to make sure that the status returned by the check is good (green) before turning the Alter to Yes.