Build a CI application alongside EE 2 installation

[eluser]Scott Boyde[/eluser]
What I have done so far is setup EE as my main site

my structure is as follows

www.nifootball.co.uk/
application - CI application
system - CI system
ee_system
index.php - ee2 index
stats.php - CI index

When I access the site I can work with EE2 as normal but to access my football stats parts I need to add stats.php/ to the url. I think I can remove this or use routes but just can't remember what I need to do.