the HTML/XML/Flash is just the mechanism used to deliver the site
i would recommend with starting by figuring out what the purpose of the site is
the type of audience you may expect to visit it and so on.
look at sites that are similar purposes see how they are structured, their navigation, and mediums they are created in.
a site can be made in many different ways that process becomes a lot easier once you figure out the goal, style and content. The format behind it can be selected accordingly
same site can be made in different ways.
if you are a coder you may find it easier to make a dynamic site using php/asp
if you’re more visual then using a tool such as dreamweaver, flash may help
html is a pretty common base no matter what path you go
and if you do not have any tools on hand
there are a lot of programs similar to this
notepad++
http://notepad-plus.sourceforge.net/uk/site.htm
makes it easier to navigate your code