Does EndNote have a Linux version? If not, I wonder whether it would run as a WINE app. (WINE allows you to run Windows based apps on Linux - it's how I use IE since my employer's timesheet website only works properly there.) I do use WINE apps on my original EEE 4g and it works fine.

You could also install a virtual machine and run Windows in a VM on Xandros.

Or go through the complicated steps of getting a dual boot scenario configured - Xandros on the SSD, WinXP on a 4gig SD card.

Or just run winXP and forget Linux?

Do you HAVE to use EndNote? Can you use BiBus instead? See this thread on the eeeuser forums.