Forum Moderators: open
If you want to submit to google/atw, just send the main page. Better yet, get your site listed on ODP and let them find you on their own. Also, a quick boost is to get your site on the Yahoo dir for 299 and then everybody will see you quickly (and you'll have a better chance of getting listed on ODP).
Also, search for "submit your site" on google for a list of places to submit to.
WDSF
Nothing will happen to Google ...or your site.
Google will find your index page, from there it will follow your links and index them too.
Once it has indexed your pages they will remain (that's opened up a whole new debate)
So fear not, submit your index and worship the cyber gods.