new user needs a little help please

Is there a way to remove the text that comes up when you upload a file with the same name, I still want the script to rename the file I just don't want the message as it might confuse my users.

Impossible at this moment, unfortunately.

Also how do I remove buttons from the tool bar eg the help button

you can do this in config.js

config.disableHelpButton

And finaly if i make changes to the script and get it how i want it, then buy the licence do i have to do all the changes again or do i just put the licence code in the config file.

You only need to enter the right license key in your application after the purchase.

On the demo of the stand alone uploaded on the ckfinder website when you double click an image it opens a light box with the image in when I double click mine it just opens a box with the file details and I have to right click and select view to see the light box, how do I get mine to do the same as the demo.

This is because the standalone sample, which you are viewing defines a custom selectActionFunction function

How where do I change the background of ckfinder, I found how to change the bar colour but not the main box from grey

?