Thank you very much for answering so quick. That didnt seem to fix my problem though :( I will paste some pictures so you can see what is happening. And im sure you will tell me how silly I am being and correct my errors :)
This is how the games look:http://img70.imageshack.us/my.php?image=amigamevf3.jpg
This is the config I am changing and saving the details to, plus I load from this config from winuae:http://img182.imageshack.us/my.php?image=amiconfigsb9.jpg
And this is the display settings in winuae I am using:http://img232.imageshack.us/my.php?image=amidisplayly9.jpg
After using Amikit I really dont want to change back to AmigaSYS, even though AmigaSYS is great. Amikit has the options I really need.
And yet again what a great package it is. :)