Take a look at this article from the BP Codex on the Template Hierarchy:
http://codex.buddypress.org/themes/theme-compatibility-1-7/template-hierarchy/
To summarise, you’d create a folder called /buddypress/ in your theme’s directory. Then a subfolder called ‘members’. Then a file called ‘index-register.php’. You should end up with:
/buddypress/members/index-register.php
Your register page’s code will go in that file and any customisations you make will take effect.
via Topic: Changing the layout of the registration page · BuddyPress.org.