I have a website in Sharepoint 2007. We use a wsp to deploy our projects. We can deploy dlls, usercontrols, features, but i don\'t know how to include new lines in the web.c
Regarding web.config files...
Web.config is an XML document that contains configuration settings for a web application. It's located in the root directory of a web application, so for SharePoint, it's usually located in the folder C:\Inetpub\wwwroot\wss\VirtualDirectories\SharePoint80, where SharePoint80 is the name of your web application.
Manually making edits to the web.config file is safe as long as you keep the the tags and sections in the right order. Look at this article.
It's also possible to make changes to it programatically, this post should show you how.
Hope this helps.