You can update your i-MSCP gui Tools by uploading them in the right directory on your server using SFTP or SCP.
But for Spamassassing, programs running on your machine, you habe to connect via ssh and start your package installer like apt or aptitude and do the update there.
I would not wait for an update of the plugin. But make a backup first. Maybe the plugin has problems with the new version.
And make a copy of the tools directories befor uploading a new version of phpmyadmin or roundcube.