your bookmarks, etc. are stored in a .mozilla directory in your home dir - and will be taken up by the new install without any problems. your settings/profile is completely separate from where you put your executable (/usr/local/seamonkey), so you should basically feel free to delete /usr/local/seamonkey after ubuntuzilla finishes its work. all your personal settings and bookmarks should remain unaffected (but of course, run the new seamonkey first, and make sure everything is there, before deleting the old one).
also note that ubuntuzilla will automatically make a backup of your .mozilla folder, so you will have a backup of your bookmarks etc. just in case.