It is uncertain as to what those percentages are relative to, i.e. because there were instances when Battery Saver reported 100% usage for two apps which simply means that those percentages are not the amount of battery % charge the apps used (because there's no battery with 200% capacity).
Nonetheless, those percentage values must be relative to a common reference. That means that those values should still give the user an idea as to which apps use the most power, which uses the least and anything in between.
The values under "App in use" are the relative power consumption incurred while actively running the app, e.g. browsing the net through Internet Explorer.
The values under "App in background" are the relative power consumption incurred while the app was running in the background, e.g. when an app has to update the live tile or receive push notifications.
Not all apps can be prevented from running in the background, that includes the Photo Hub, Outlook, Messaging... etc - these can all be seen under both "show all apps" and "show apps with usage". However, so that there will be less confusion, there is a third option to "show apps that can run in the background". These are all the apps which the user can toggle on or off.
I'd recommend you to select "show apps that can run in the background" from the first underlined clause underneath the large "usage" title.
Hope this helps.
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