Even with the latest firmware, the R44 marking system still works on the basis of having 99 markers preset for each file, placed at the beginning of every file. When you place a marker during a recording, the current time is added to the data for the next available marker. So if you place four markers, in your editing software you will probably see 95 markers at zero time, and 4 markers at the times you pressed the button. They also show in most other software.
The markers show in Reaper, which is an excellent tool for post-processing live recordings. If you want to get rid of the markers that the R44 parks at the beginning of each file, in Reaper you can simply shorten the left edge of the clip by a tiny amount, so that the markers on the original left edge no longer show up (they're off the left end now).
There is a command in Reaper to convert the markers currently showing in clips to project markers (instantly), and you can then go through and give these project markers names (eg the titles of the songs). Using a little utility called "ReaBurn" (written by yours truly, google will find it) you can then automatically create a cue sheet which includes these named markers and burn a CD with appropriate CD text.