Site maintenance/merge changes I set up an account at BlueHost and my unfinished site is now live at columbiablooms.org.

My understanding is that when I make modifications, such as enhancements, that changes are made not only to the file structure, but also the database meaning that from this point forward I need to make all my changes and content additions to this live site. Also, I want to be very careful to backup both the file structure and the database before I make changes in case I mess things up.

At this point my Acquia Dev Desktop is not very useful since there appears to be no way to merge what I've done on my local machine with what's live out there on the web.
You aren't required to make changes directly to your live site, it is bad practice to do this for things other than minor content additions/changes.

You should have at a minimum a dev and production environment.  Your local environment would be dev obviously and there are many ways to sync the changes between dev and live.

If you have ssh access to your server, the best way would probably be to use drush to sync your changes between environments.  There is a good explanation of this method here.

If you don't go the drush route, you could always do it manually by dumping your local db / files and updating the live site.

There is a lot of information on the subject on this site, a good bit of info can be found here.