The key that you have to understand as well is that any customized site can be saved as a template and reused as 66866 described. If you are strictly going to use templates internally on one farm it's the easiest way to do it.
The WSP files Microsoft created are Sharepoint Deployment Solutions as a installation distribution mechanism. If you are going to sell templates or distribute them to other Sharepoint farms it's a viable option.
Here is the methods to customize from easiest to hardest
1) Use the Sharepoint UI to customize a site
2) Use Sharepoint Designer to customize a site (Designer makes it easier but isn't mandatory)
a) Customize a web page
b) Customize site shared content like CSS, images, layouts master pages
c) Add Data View Web Parts (requires designer)
3) Use Visual Studio to create
a) Custom workflows
b) Deployable custom web controls in page layouts/master pages
c) Deployable custom web parts
d) Entire WSP solutions for new site features
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by: 66866Posted on 2009-03-14 at 06:59:25ID: 23886880
It depends on what you want to "customize".
If you want to make changes to a List, like add/remove columns you can make those changes using the List settings. If you want to change the structure (let's say the layout style, formatting, conditions, etc) you'd use the Sharepoint Designer. If there are any built in workflows that can be modified using Sharepoint Designer you can do that as well. You use Visual Studio only to build custom web parts, workflows, applications.
Designing templates can be simple and complicated. A simple way would, going to the "Site Settings", under "Look and Feel" and selecting "Save Site as Template" and this would save it as ".stp" file that you can use for creating similar sites within the same site collection.
Here's a white paper from MS that talks about how to create these template solutions
http://www.microsoft.com/d