Basically, you just run the beer from one keg to another, placing a filter in between the two. Detailed instructions come with the filtration kit. This is done BEFORE the beer has been carbonated. There are three different levels of filters, coarse, fine and sterile.
The most efficient way to filter is to have your two kegs, insert the coarse filter in the housing, run your beer from one keg to the other.
Then insert the fine filter in the housing, and run the beer back into the first keg.
Now insert the sterile filter into the housing and run the beer back into the other keg.
This should result in a very clear, sediment free beer that will taste great.