Here is how I do some of the things you ask. I also have a development site and a live store site. This allows me to make the changes I want to try and then when I get it fixed copy those files to the over rides directories in. This allows my customers to only see the new look after it has been tested and known to work.

I made a back up of my database and put it in a new database. I keep the test database updated every week so it reflects my live site. That way I have everything the same but don't screw with the original during development.

I use Yummy FTP (Mac Program) to compare folders remotely. If I make a change locally it adds that change to the server automatically. Good for keeping the pictures updated as my wife adds product everyday or so.

Learn to use the over ride system. Here is a good chart.

http://www.zen-cart.com/index.php?ma...roducts_id=298

I use it and can keep track of changes I make much easier. Less searching for files I changed. This structure can also be tied to yummy ftp to update your server when changes are made. I don't allow this to be automatic because I don't want anything ot be uploaded that hasn't been tested fully.