As I understand it should work from the usb without problems. I think it really is just a kind of script which replaces one ipdf executable with other. Even if you unplug the usb, the version you last choosed should be kept and work ok.
For column mode I prefer alanine's version, it feels more intuitive to me. But the anotations are not shown properly. Well, you can annotate, and the annotations are kept and you see them ok when writting them. But if you want to review them in column mode, they don't show properly. You'll see. I will try to fix this as soon as I have some time to deal with the develpment environment ;-)
You can merge the annotations in a new pdf in the computer with this great multiplatform java application ->
https://www.mobileread.com/forums/showthread.php?t=9535
Enjoy your papers!!