The number of widgets shown is the total number of widgets your members have on their profile pages and dashboards (either added by themselves or added automatically in case you defined a set of default widgets). Each member has their own instances of the widgets to allow for personal widget settings. It's nothing to worry about.
For configuration of the index page you can for example use the Widget Manager plugin (http://community.elgg.org/plugins/384604/4.3/widget-manager) or the Homepage CMS plugin (http://community.elgg.org/plugins/968182/1.2/homepage-cms). For a plugin to change the logo you can use the on-site search function ("logo"). There are several such plugins available.
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