In all probability, you will want to create a new site definition and
implement your design as a master page.

I need more details.. Any
tutorial or anything to show how? where to put my master page?

check that:

blogs.msdn.com/.../creating-and-using-a-minimal-master\
-page.aspx
blogs.msdn.com/.../building-tylerbutler-com-part-1-pla\
nning-and-basic-branding.aspx

for a good introduction on master pages.

I want to use a custom site template  when creating a new top-level
site. I read that a site template can be placed in the central
template gallery using a command line tool on the web server ...

- where is the central template gallery; how would I navigate to it
- what is the command line tool or statement for accomplishing