Upgrading Vs Clean Install on a custom config.

I am Running 7.10 currently, and this next release will be my first upgrade. I have some custom scripts that run during startup that deal with dual monitor support, (Ubuntu still didn't get it right in 7.10, fingers crossed for 8.10). and a manually edited xorg.conf. I read one of the upgrades was xorg. I'm pondering what would be the safer way to go. Clean install or Upgrade? I'm afraid I may have changed enough things that an upgrade may not work. I don't fully understand what upgrading actually does. I find the term 'upgrade' to be slightly confusing, and was hoping for some clarification of the actual upgrade process. When you run the upgrade does it just upgrade all the individual files, or does it act more like a clean install, but your home directory remains untouched (similar to a MS OS upgrade)? Does it replace your /etc directory, does it still load your session settings from the old version, etc.

Should I anticipate problems with running the upgrade with some scripts that run, specific to the version of xorg thats installed currently?

My main concern is a failed upgrade, then dealing with the recovery after the fact. I would rather take the Long and Safe route vs Easy and Broken.

Any advice or anyone who's had any experience that they could pass along would be most appreciated.

thank you,

Keith