I know silent install is ran with *-setup.exe /sp- /silent /norestart
Silent install with no prompt is ran with *-setup.exe /sp- /verysilent /norestart

But how do I predetermine install options?

Meanwhile, if this is an update and not a first time install, will it be like the unsilent install that remembers the old install's settings?

Finally, I wish it wouldn't automatically put a file in the RUN key, but I guess that must be deleted manually.

you can't predetermine the install options using clamwin installer. You can however copy all needed file manually. The install script for your reference is in the SVN source code repository.

An upgrade will not overwrite existing settings.

ClamwTray.exe is an essential component of clamwin (re-iterated in the forums couple of times) and disabling it in the Run key shall only be done with understanding of all consequences, search the forums for more information.