Back to the multiple installtions of wiki. Here is what I did.
In installing the second wiki, lets say wiki2. I symbol linked everything from the first installation, except file LocalSettings.php and directory config. I Created it’s own config directory. Then installed the second mediawiki using different database.
The benefits are you do not need to keep many shared files/directories.
Another insteresting thing when playing with mediawiki. How about just two installations sharing same database. NO PROBLEM. You gained a lot by sharing many common files/directories as well as database. I checked that mediawiki databse diffentiates the data from two places pretty well using unique Ids so that if you browse one wiki it will not show up wiki you configured in another place. Nice feature.
However, if your wiki tends to be really big, you may choose to install it in a separate database though.