This sort of thing can be very stressful when you do it the first few times.
I assume you are on a dedicated server?
You might consider installing Virtuozzo (or openVZ) for your next server. Even if you only have, say, one or two "Containers" (VPSes), it makes recovering from errors easy because you can backup and restore the entire VPS in a matter of minutes.
For example we have one Container running Plesk 8.2.1. It was time to upgrade to 8.6.x. I went through the upgrade motions and BANG - serious problem, Plesk borked. I could have spent an hour or so possibly fixing the borked upgrade, or possibly I would have failed. Instead I checked what had gone wrong, then restored the Container to the backup I had made just before trying the Plesk upgrade, fixed the problem that had caused the problem, and upgraded again. It all took 10 minutes and everything was fine this time.
Of course there are other ways to backup and restore that don't involve using virtualisation! e.g. 4psa's Total Backup, or just manually dumping databases and tarring directories, or using some other form of backup. In fact lvalics has a nice script that a few people have been using that backs everything up for you.
And when playing with things that might go wrong (Plesk updates in particular), backups can be a life saver.
I hope all goes well for you -- it should. You are not doing anything too dangerous. It is just necessary to make sure you have backups of the important config files in order to prevent things going horribly wrong if you do encounter a problem.
Faris.