You are making work for yourself. Much better to stick with the installer until you know what you are doing.
If you want to carry on then you need to install the alfresco.war file into Tomcat's web apps folder.
And you also need to "put back" the "extensions" folder that was removed in Tomcat 6.
Change the classpath and increase the memory settings.
You will find more details in the install guide, on the wiki and in these forums.