I'm also using 10.6.x. However, since I don't know the difference between the ecoreader and the bebook, it's hard to say.
I have had zero problems with loading anything to the reader, either to the SD card or directly to the reader's memory.
In general, there would be no problem with the method of disconnect from the Mac assuming the copy cycle was done. Normally you'll get the progress bar in a dialog box saying "copying from X to Y" and below the "thermometer bar" you'll get notification of time. remaining.
The ONLY problem I've run into is that the bebook creates blank files with the name of the book prefixed by an underscore. Example, "_Call of the Wild, Jack London". These files are ALWAYS located "in front" of the real files, no matter the sorting method. I haven't yet learned to remove them, since they're a PITA and contribute nothing.