This is how I solved that problem:
I have a FAT-32 partition called Data where I keep my Notes data directory and all my documents. This partition is mounted automatically by my user ".profile" under my Documents directory on Linux. CrossOver sees it as Y:\Documents (Y: is /home/<my_user> on CrossOver).
I have two Notes 6.5.3 installs, one on Windows and one on CrossOver. Their respective notes.ini files point to "D:\Notes\Data" and "Y:\Documents\Notes\Data", whcih is the same actual directory. Also, my mail file is always pointing to the local replica, not the server replica.
In order to avoid conflicts between them I have four Notes Locations: Linux Island, Linux Network, Windows Island, and Windows Network. On each location, the settings point to the same files but with the apprppriate paths depending on the OS. On the Windows Location files, paths are "D:\Notes\Data\..." and on the Linux Locations paths begin with "Y:\Documents\Notes\Data\..."
As for browsers, my Linux Location files point to Netscape Navigator. This passes http calls to CrossOver. Now, on CrossOver itself, my preferrer browser is set to "firefox", which refers to /usr/bin/firefox. This allows Notes to launch my Linux-native firefox whenever someone sends me a URL link on a document.
This setup allows me to switch to Windows when I have to and still be able to check my mail. Notes usage on both environments is transparent. I have no complaints.