1. if i root with unrevoked and put S-off will this effect my settings or layout?
No
2. is rooting the only way to make complete backup?
Yes
3. if i make backup, is it making the backup with root included? if i decide to go back to bone stock and load backup, will it be rooted
No, if you go back to true stock by downgrading, it will remove root. But...see #4.
4. can you even load a backup copy if you revert to bone stock.
You can do a Nandroid backup of the stock ROM when you first get it and it's rooted. Then you can always go back to it although to be honest, there are superior "stock" ROMs out there that are almost the same thing but some worthy enhancements included.
5. can titanium backup accomplish what i am wanting to do?
Titanium is mainly for backing up apps and their data. You can back up system data as well, but when crossing ROM's it's not always prudent to restore system data as conflicts can occur.
6. to clarify what i am wanting to do.
A. make a back up of stock existing layout, settings, etc.
B. keep or load a back up of all my apps when i root
C. keep or load a back up of all my apps when i load custom rom
In short, use Nandroid to make a carbon copy of everything on your phone at that exact point in time. That includes the works. These are handy for reverting back to an exact setup you liked and also provides a safe place to return to if things ever go south in a flashing attempt (bootloop, etc).
Titanium is great for replacing your missing apps and their data when flashing to a new ROM. Go get Titanium from the market once you're up and running, load it and it uses reference files on your SD card to know it's you and restore your apps and app data.