is it possible so that say someone chooses the package named "free" on my website, a banner is automatically added onto the top of all their pages, but for ones like bronze, silver and gold package, there would be no banner inserted?
That's where you would put the code in the /home/username/.htaccess files so it only applies to the accounts that have the code written to it. The drawback to that is, either the client can modify that file to remove it, or it has to be read only for the client which means they can't use it for anything else. For free hosting they don't need use of that file anyway.
Change append to prepend to put your file at the top.
I'm not positive about the proper way to write protect the file, but I would just do "chmod /home/username/.htaccess 0444" in shell which would make it only readable. If you ever want to change it you would have to put it back to 0644. It might also work if you leave it at 0644 and do "chown root /home/username/.htaccess" which would make root be the owner and therefore the only one who can modify it.