It is not recommended to change a downloaded plugin, this will cause problems when you want or need to update that plugin.
-
You could consider extending the plugins’ class when it has one, in another plugin, for this you will need some PHP knowledge. This way you will have two different plugins, yours, and the original plugin wich still is able to update.
-
You could try to build your own plugin looking at the source of the WordPress Popular Posts plugin.
-
There are plenty of plugins avalible in the WordPress Plugin Directory, I’m sure there will be one that fits your needs.
I would advise you to not try duplicating a plugin installation but search for another solution, such as I mentioned above.