DFSEE can do whole volume, or whole disk, images, but they need to be restored as a complete package, you cannot pick individual files or directories (Acronis would be the same, when backing up OS/2 volumes). The other problem is that it will restore to the same size, and geometry, not allowing changes, so you end up with exactly what was backed up, losing any interim changes. I highly recommend using DFSEE to do the Disk Analysis thing, and save the results (as prompted).
Since BackAgain/2(000) has become totally unreliable (it backs up okay, but it won't restore properly, in all cases), I have been using ZIP to zip up whole volumes (including active boot drives). It is easy to simply format a volume, then unzip into it (size and geometry don't matter, as long as it is OS/2 compatible). Sometimes, I need to use SYSINSTX, but it has always worked, for me. I use that method for boot drives, but I do make sure that they contain ONLY the OS. and a few other things that don't matter. I also ZIP up my programs/data drives, but that is a secondary backup. You do need a version of ZIP/UNZIP that can handle files that are larger than 2 GB, if you have files larger than 2 GB, or if the resulting zip file is larger than 2 GB. Note also that this is NOT an incremental, or differential backup solution.
For my data/programs volumes, I also use RSync to copy to a USB drive, and a LAN drive. To extract individual files, or directories, I just need to attach the device, and copy what I want. USB, and LAN, is slow, so if I ever need to copy a whole volume, I would probably remove the drive from the USB enclosure, or the LAN machine, and attach it directly to the computer. This is also not really an incremental, or differential, backup solution. It always produces a full backup by replacing, adding, or deleting, files to match the source. After the first pass (where it has to do all of it), it simply does the changes, so it is very fast.
I do use the Seagate version of Acronis (free, but you do need a Seagate, Maxtor, or Samsung drive attached - can be USB, IDE, SATA, SCSI, SAS, but not LAN) for windows backups (Look for Seagate Disk Wizard - it does not have all of the features of the full Acronis program, but it works well). There is no doubt that that is the very best windows backup (the ONLY one that actually works for windows, that I know about), but it is probably not ideal for OS/2 (if it works at all). Be sure that you don't let it mess with boot records, or it could mess them up.