I have recently updated my server (or rather had my hosting company update it) - twice. In total the server configuration had to be recompiled 3 times, causing a bit of downtime - but all in all it looks like it's finally in good shape.
Prior to the first upgrade I was able to specify site-specific php parameters in the .htaccess file or the php.ini file (properties of which I have mentioned in other posts). I lost this capability during the first upgrade - thus I had the site re-compiled so that I would have this capability once again.
The update caused 4 of my sites to crash, but after getting them back up, here is what I have learned:
* php.ini is where I have to put all of the php_values from now on - these are all the max files sizes, post sizes and so-on.
* .htaccess files in older versions of drupal don't work. I have to update them with more recent versions. You can (or must) still specify all of the RewriteEngine stuff in here.
* All files must have the permissions of 644, and all folders must be set to 755.
* The files and folder must be owned by the user of the account that the files and folders reside on. ( I have no idea what this means).
That is what I have learned.