Show 125by125 ads

Hi,
I have just now shifted to wordpress and have installed the latest version i.e 2.8 and I am facing some problems with placement of ads in the theme ( Monezine ). Although it has built in feature to place codes however i am not able to use google adsense to display either 125×125 or 300×250 ads. It asks for banner url and all i have is a javascript code. Can you help me with this or maybe refer to some site or tutorial.
I will really appreciate if you can manage to do so.
Thanks