At the end of the upgrade, all your users, pseudo, groups, mail settings, ibays, ect are there, intact. Nothing is lost. So doing a restore from the old 5.6 will not achieve anything - it will not fix old contribs not supported by vs 6.
Check each contrib and ascertain whether they are OK with Vs6 - some are. leave them alone. For contribs which are not suitable, whilst you may get away with a reinstall, you may as well get rid of them before upgrading, then reinstall a suitable version after the upgrade.
To be safe, backup to desktop + make a re-install diskette. If all fails, you can re-install 5.6 from CD ansd restore, nothing is lost. Another way is to "ghost" your drive, and upgrade the copied drive.
I have logged a number of upgrades, can pass you the document off line for info, its quiet simple. chris.