I've now completed 14 SPS 2003 and WSS rollouts and have found the following as a best practice:

If you are building a corporate portal on a dedicated server, etc., rather than on a shared SPS/WSS install, then you can load the actual code pages [.aspx files] in to VS.Net and modify them from there. It's not as clean as being able to open SPS or WSS as a VS.Net project, but it's the only way I've managed to do it.

When you use this method you can completely rebuild the SPS or WSS pages as you wish, using all your design skills, etc.

The only downside is that once you change a page it will effect all others using that template or code page. You can get around this by creating seperate templates/themes for each department and moving on from there.

If you are using a shared server, i.e. a WSS hosting solution, then you have to use FrontPage 2003 for your changes. The reason for this is that, when you click the save button, FrontPage 2003 makes SPS/WSS save the page in the database, rather than relying on the underlying code page. This is where you get in to un-ghosted pages, which can be a real pain when the boss decides to change a company logo or something.

Other thing you will notice on WSS are:

As soon as you hit the save button in FrontPage 2003 the watermark down the left completely disappears!

You can modify the site navigation on the left and then close FrontPage 2003 [with out saving] and the new links, etc. appear on the WSS site!

NB: Once un-ghosted you either have to delete the WSS site or SPS area, or find a webpart that will show you which is which and re-ghost the site/area. There is also a field in the database which keeps track of this, but I can't remember where now.

Have fun...