Help needed with working around the limitations of Site Sculptor

First of all, when I say "limitations", I don't mean that in a derogatory sense, just as an observation as it is what it is. Having created a couple sites with Site Assist Pro, this is my first one with SS and the CMS. Just to get familiar with the features, I published a basic version of my site and the CMS set-up was without problems and the editing tools are just awesome. But now that it's time to build the real site I'm finding myself tripping over a few things and welcome any suggestions by my fellow developers as well as the support team. These issues I'm sure are not unique and perhaps will be addressed in a future release or chapter two of a Getting Started guide. This is my workflow, and I'll point out the places I find a little confusing.

Starting with CSS Sculptor and CSS Menu Writer
I built a home page and a content page starting from a pre-set layout and modifying to my needs. I created the menus for each page with Menu Writer and inserted them into the div containers where they belonged into the CSS Sculptor generated pages. I saved two copies of each page - one with the menus and one without. I will only need one version of each, but I'm set depending on which direction I take from this point.

Saving as Templates
Deciding to follow the WA guidelines in creating a Site Sculptor design, I'm going to use template files in lieu of CSS Sculptor presets, so I saved the homepage and the content page as templates. The versions that I saved as template files did not contain any CSS Menu Writer menus. (This particular piece of information does not present itself until later when you're in the Site Sculptor dialog creating a new site design and are attempting to select a template with a Menu Writer menu. But it doesn't halt your progress, and I didn't carry it out to see what would happen) Should template files be saved as *.dwt or *.dwt.php?

Adding Editable Regions
Now, one challenge is presented in that both the homepage and the content page are to contain three menus - a top nav bar, a secondary nav bar and the footer. There is no practical reason to have any of these regions editable, but apparently they need to be in order for Site Sculptor to work. Is that correct?

Best way to configure Site Sculptor
So now I have my templates set up, with all three menu divs as well as various content divs editable, I launch the SS Preset manager and add a new design. Given that I will have three menus and the options allow me to insert one menu region, one content region and the footer - same for both the homepage and content page, what is the best way to configure this?

I would like all pages to be included in the CMS including the homepage. After the site is generated, I can go into the new content page template to add additional menus and make any other modifications to the layout. But there doesn't appear to be a way to do this for the homepage! SS doesn't generate a homepage template and the index page layout can't be edited in Dreamweaver. So, what is the workaround for this? Is there a way to make the content visible on the index.php page to add the other menus or make other layout modifications? Or can this be done using the online CMS itself? Is there a way to manually implement CMS capability to the original homepage? The only other option I see is to not include the homepage in the CMS.

I wouldn't be surprised if there was some simple setting that I'm missing and I've written a bunch of stuff for nothing, but thanks for reading!