If I understand you correctly you found the conboy folder on your n900 but when you access your n900 via USB with your ubuntu rig you cannot find the folder? On the n8x0 conboy notes are kept in /home/user/.conboy I imagine the n900 is similar in setup. I have not used usb storage mode in a long time so I'm not sure if it mounts /home/user/MyDocs/ as root instead of /. If so that would make it hard to get to the conboy notes folder.

What I did before using conboy's excellent Ubuntu one sync is rsync over a ssh to sync up my tomboy and conboy directories. You can install the openssh server on your n900 and sync that way over the network (much more convenient than usb storage mode IMO).

However, since you are using ubuntu I suggest you give the built in sync in conboy to sync your ubuntu box and n900 notes via ubuntu one. If you need setup help for this let me know.