How to backup boot partition or system config?

I have been pulling my hair out trying to figure out the best way to backup my boot partition.  well not only the boot partition, but also /data/.apps/.  I'm just running into one road block after another and the end result is I don't feel like its adequately backed up.  I appreciate any and all suggestions.  Here is what I have going now and some of the issues.

1. I use iDrive to backup any shared volumes with the business data on it.  that works fine.  Unfortunately iDrive does not preserve owner perms in the backup, but its just me using it, so its generally not a problem.
2. iDrive can also backup the /data/home volume, which is hardlinked to /home.  This backs up my one and only home dir, so again, shouldn't be a problem, everything in there should be owned by me.  
3. Everything else at the root level is not backed up, iDrive can do it via command line scripts, but will not preserve owner perms anyway, so I'm looking for another way to backup that stuff.  /etc, /apps  (which is really /data/apps), /root, /usr/local, among a few other things.  
4. I have tried rsync and rsnapshot, but all my other machines are macs and I have run into never ending rsync errors that don't make sense to me, must be because of different architectures.

How do you people backup your configured readynas?  After all this time installing custom stuff with apt-get, compiling some stuff from src into /usr/local, a few tweaks under /etc, some startup scripts, config files under /apps for various servies like headphones and sickrage, for example....  its not backed up.  What's the best way to back all that up? iDrive can't do it.  ReadynasVault can't do it either.  Is it even possible to backup a readynas device in such a way that it can be restored to run again in the same condition as now..in other words...all the installed software up and running as before?  Backing up the /data volumes is easy...as long as you don't care about owner perms...but backing up and potentially restoreing a working readynas at the root level for all the software.....  I am at a loss for how I might approach that.

Secondarily, I could just keep a backup around in case a file gets accidentally deleted or something...  for that I could probably just rsync -a the root stuff into some other directory under /data and then it would be there for that...or better use use rsnapshot to have timemachine style recovery of individual files.  That is probably what I may do, but I am wondering what other people are doing for that, and for the possibility of having to restore the entire working machine somehow in a catastrophy