My upgrade to OS X 10.11 El Capitan was not the smoothest of experiences, but I did not develop an attack of sweaty palms – so it could not have been all that bad.
This is a big download, especially if you have a small bandwidth connection. At a tad over 6 GB, even the lucky folk with very high speed connections will notice it downloading. However after a few hours on my 3 Mbps link here, it all came down. A few users have found that the download gets broken, in which case you will just have to try again.
I left mine downloading overnight, and it was ready to start installing when I got up this morning. However you need to allow ample time for that installation. It looks like it does a lot of file moving, and some users will find that parts of the installation will take very long periods, even a couple of hours or more.
As I reported earlier, the progress bar is a very unreliable estimate of outstanding time to install. In fact I lost time estimates altogether for the last and longest phase.
If you cannot hear disk activity, and the installation has been running for at least an hour or two without any change in the progress bar, you can try pressing Command-L to get it to list what it is doing. I found this unreliable, but when that works it can reveal that the installer is still working furiously even though you might think it has ground to a halt.
If you are completely convinced that it has stopped, and your Mac appears a lost cause, hold the power button down to shut it down, then start it back up. I had to do this very late in the install when the progress bar was getting close to completion, but nothing had happened for a couple of hours (we went shopping!). Chances are that when your Mac starts up again it will resume the install correctly, and all of a sudden it will be back again.
In recent major upgrades like this, these long delays have been the result of the installer moving everything in hidden folders such as /usr. Most users have little tucked away there, but some can have huge packages such as Ghostscript, which make those moves very slow indeed, as each file is copied out, one at a time. I suspect that to be the case with El Capitan too.
Remember that once the installation has completed, the installer will remove itself. If you want to keep a copy, in case you need it again and cannot face the download time, then you must make a copy before you start the installation. However if you have Time Machine running, and it makes a backup between the completion of the download of the installer and the start of the installation, you will find a copy in your backup.
Once you are back up and running, verify that your key apps are all working properly, and then check your logs in Console. You may well come across the plaintive cries of some broken services, which you will need to address. It is also sometimes worth trying a restart to see if that helps the logs go quieter.
So far everything seems to be working OK, but neither are there any great surprises. I wish you success in your upgrade(s).