Saving documents to DT

I have been experimenting with storing all of my files and folders in DT and indexing them. I finally decided the storing the files and folder in DT was the best approach for me because it avoids the constant need for synchronization. However, I have run into a problem.

First, it seems that I have to save a new file to the finder before I can save it to (or import it to) the database. I can understand why this is might be necessary since, as I understand it, the database is sort of a file structure within the finder so that files must exist in the finder before they can exist in the database. However, once the file in in the database and I have eliminated it from the finder, I can open it in the original application, but I cannnot save any changes. Or, when I make changes and save, I get a message that the file is in the trash, which seems to mean that the file does not exist in the database at all. This seems to mean that I must still retain a parallel set of files and folders in the finder. But then, am I doubling the volume of data on my drives? And what is the database really doing for me other than allowing me to more easily preview some types of files?

If I use indexing, I have to constantly remember to synchronize, or the next time I open the database, I will not see my latest changes.

I am obviously missing something. Can you help?