If you want to change webquickstart design you can, just by overloading css files and include it in your page like this :
Go to your tomcat/webapps/wcmqs/css folder, create a new folder, duplicate the general_styles.css, rename it and put it in this folder.
Open the index.css file and include your new theme :
@import url("reset.css");
@import url("typography.css");
@import url("general_styles.css");
@import url("slimbox2.css");
/* these are the available themes: uncomment the css for the theme you want to activate */
@import url("foldername/cssfilename.css");
/*
@import url("white_blue/styles.css");
@import url("white_orange/styles.css");
@import url("white_green/styles.css");
@import url("dark_brown/styles.css");
@import url("dark_orange/styles.css");
@import url("dark_redblue/styles.css");
@import url("red_brown/styles.css");
@import url("krem/styles.css");
*/
There you are able to overload wcmqs css styles through your new css file.
If your design is completely different you'll have to create your own templates :
In webapps/wcmqs/WEB-INF/templates you can create your own page structure and specify region for your webscripts.
In webapps/wcmqs/WEB-INF/pages you can define webscript call in your template regions with a simple xml file.
In webapps/wcmqs/WEB-INF/webscripts you can create your own webscripts.
In Alfresco Share you can specify wich template instance you want to call on section indexPage or on article visualisation, just set it in your section metadatas.