GD Press Tools Pro 5.0 is created with multisite support at its core. In the multisite mode, plugin main control is inside the Network admin. Some features and addons can be controlled through Network administration, and some can be set for individual blogs in the multisite.
Network Controlled Features
Addons like Tweaks and Cleanup have a special set of tools for use in Network admin. There several tweaks that will be available only in Multisite WordPress installation. Same with Cleanup, some cleanup tools are Network only. Debugger, Toolbar Integration, and Events Log are Network controlled. Some features and addons can be controlled on the Network level, but super admin can allow overriding them on the blog level (SMTP Tools).
One very much unique feature in GD Press Tools Pro is something called: Overload. In Network mode plugin adds a second top level menu called Overload. This mode allows you to control blog-specific features from one place for all blogs in the network.
What does this mean for the plugin setup? Take the Tweaks for instance. There are 60+ tweaks you can set, most of them are for blogs and not the whole network. So, you need to go through Tweaks panel for each blog in the network and set (usually) all the same tweaks. Well, with Overload this is no longer the case. In Overload Tweaks panel you can set some tweaks, mark them for Overload and they are applied to all blogs in the Network! And, they will not be available for use on the blog Tweaks panel. Same goes for settings, Post Duplicator and WP Dashboard addon work in Overload mode.
Backup works in a multisite mode in both Network and Blog admin. In network admin, you can backup everything or only selected blog. In blog admin, you can backup data for current blog.