google websmaster and analyticator

I installed the google analyticator plugin in my wordpress site. I also have the all in one seo.

I read something about using webmaster tools to verify your site. I did that and now it says my site is associate with a google property.

I then realized that in my all in one sep pack, there is a place to put in my google webmaster info. I tried but it won’t let me verify again. did I screw up by associating my account in google webmaster tools? is the google analytics that it is now connecting to going to override my analyticator plugin in my site?
I hope I’m explaining this correctly.