I would try the upgrading on my local machine at first, after that is successful, then upgrade on the server machine.
With these steps, I will have no chance to mess up the real site.
do you want add third tables with different table_prefix in the same database?
I mean that you want use two different wordpress systems, but use only one database. There are wordpress tables with two different table_prefix in one database.
Am i right?
I try this, it works!
.htaccess file always auto created. If not, you can create it manually with empty content.
Then just put the code into the file. Maybe it can work after these.
I do not know how to write php script either, but installed wp successfully, just spend less than 5 minutes.
5 minutes means you should know how to install a php engine and a mysql database.