Hi Tom,
There are two ways of preventing your site from being upgraded before you are ready, one is to set <add key="AutoUpgrade" value="false" /> in your web.config, the other is to create a file called app_offline.htm with some blurb explaining that the site is being upgraded and put it in your root folder. 1) will simply stop an upgrade from happening, 2) will prevent the site from being accessed at all. If you have forums or other modules that accept data and store it in the database, use 2) Actually, you should probably use 1) and 2) for all upgrades, if this isn't the case, I'm sure someone will chime in.
Now BACKUP YOUR FILE SYSTEM AND DATABASE.
As you are using 4.9.4 you can unzip/ftp the upgrade package over your existing file system. There are reported problems of the built in decompressor not unzipping the files properly so use something like Winrar or winzip to do this.
You don't need to make any changes to web.config, the installer will look after this for you, your permissions shouldn't need to change.
If you created an app_offline.htm file, you should now rename this (it doesn't matter what to, the site will start once it's not there); you should now browse to http://mysite.com/install/install.aspx to kick off the upgrade.