With the Android version, the menu icon on the bottom of the screen will also bring down the File Manager menu.
A few tips to get started:
Once you have navigated to the beginning of your library, you might want to "long press" on the link to that page (the "./" at the top of a page that you can select from the beginning page) and you should be given the option to "Set as HOME directory".
(That is an example of one of the conventions used; A long press on setting options will often let you set that option as default. This is used for many of the menu items.)
On my 10.1" tablet I set the Progress Bar to "Full" [bottom menu, gear icon] and long press that to make it default. Then I go to [top menu, gear icon] "Status bar" and uncheck "Current page", as it is in the header for the "Full" progress bar.
You will probably want to set the "Screen" [top menu, gear icon] options, unchecking "E-ink optimization". You might also want to set the "Screen DPI" to match your device. Long pressing the "Custom DPI: 160" brings up a window to set it as you want. (Your Nexus 7 appears to be 323ppi)
One of the most useful features is the "History" menu item. It provides a listing of your previously opened files, with your current read at the top of the list. Selecting an item brings you back to wherever you were in that book. [ One thing I do on occasion is to extract the maps from an .epub or sometimes, download a better map, and convert them for display on my device as PNG files. Once I've opened them, they will appear in the History, along with the book. I can then, leave the book and go to History and select a map. After looking at the map, I can got to History again and select the book, returning me to where I left off.]
Oh, I should add that, for PDFs, you can set the default to "Zoom to fit content" by long pressing on that selection, of the "Switch zoom mode" menu item.
For adding fonts, dictionaries, and hyphenation dictionaries,
see this post
For many of the menu settings, a long-press should get you a message box with the option to set that selection as the default.
The "Advanced Settings" menu presents you with many options that you can set/change by poking the all uppercase name of the option. This should give you a message box and keyboard to make the setting(s).
After making changes, upon leaving Koreader (Pressing the Home Icon) you should get a message box with: "You have unsaved default settings. Save them now?" Press "OK" and hopefully you will see a new message box with: "Default settings were saved successfully!"
That should be a start.
Luck;
Ken