To use filters you first have to understand profiles.
Multiple profiles can be set up for single site AKA a single tracking code and a filter is used to filter data for 1 profile, a profile can have multiple types of filters but it'll still do something for only 1 profile. Also the filters are re-usable.
You can approach this question in several ways:
- You can set up multiple profiles, each with it's own directory filter. However in GA you can't measure only the index site's traffic with clean urls.
- You can set up advanced segments. This way you can easily compare statistics. But you still can't measure the index site's traffic if you've got clean urls.
- See the Content -> Overview
Using the page exact match can result in some interesting side effects:
- It'll show you the statistics of the WHOLE site, as / is the root of the page
- Also it can show you the statistics of all the urls which has a / in it