1,2,3: This is exactly why reading the instructions on the email with your license key is so important. From the text in the email with your Nexus Ultimate license key:
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How to download and install Nexus Ultimate:
You DO NOT need to uninstall the free version of Nexus if you are
currently running it. Nexus Ultimate will automatically convert
the free version of Nexus into Nexus Ultimate and your settings
will be preserved.
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Anyway, Nexus free, Nexus Ultimate and Winstep Xtreme can be said to be 'extensions' or 'evolutions' of the same application. That is, Winstep Xtreme > Nexus Ultimate > Nexus free. Nexus Ultimate does everything the free version of Nexus does and more and Winstep Xtreme does everything Nexus Ultimate does and more. Click
HERE for a product comparison.
All the different 'flavors' use/share the same files, folders, etc, including the same 'slot' in the Add/Remove Programs applet.
4. The installer for Nexus Ultimate will automatically delete the free version of Nexus (and the shortcut to it in the Windows Desktop) if it finds it and replace it with Nexus Ultimate. If that didn't happen in your case you must have done something unusual such as installing Nexus Ultimate in a folder other than the default folder.
Go to
C:\Program Files (x86)\Winstep\
and delete nexus.exe if you find it.
Before you do that you might need to figure out which version you are running. Why do you say clicking the Nexus icon on the dock opens the free version? Do you see the About tab of Nexus free Preferences when you do that? If so, then you are running the free version of Nexus (nexus.exe) and not Nexus Ultimate (nexus-ultimate.exe).
6. Inside the Tile Pack zip file there is a README.txt file. Please read it.
7. By system icons do you mean the system tray icons or something else? If the former, under Nexus Ultimate you have a Tray tab in Preferences. It has a Customize Tray Icons button - click on it to 'replace' the system tray icons displayed in the dock with your own higher resolution versions.