As soon as I open wine all windows are half screen and I cant change them. The graphics are as low as it gets and I cant even change them in system settings.

I am not sure I understand you correctly.

If you mean that the window of the program that is running on wine is too small, wine can't do anything about that. Some programs, and almost all the games, set a given screen resolution. Sometimes you can change it on the game setup, sometimes it's possible to do so by editing a given ini file or a key in the registry. It depends on the program.

Wine can't "zoom" windows magically if that's what you were asking.

However I think that compiz-fusion has a plugin to zoom windows, never tried it though.

If I open "configure wine" The window size is bigger than the screen but the window border is smaller than the screen. I cant change anything from there because the window wont move to let me click on the proper box.

If I go to the "system settings" from the Kmenu and select wine from there, it takes me to a configure screen similar to the one in wine but none of the changes I make in there effect wine in its own window.

Its not just configure wine that does it either. If I try to install a program in wine all install boxes appear the same way. All windows outside wine are normal