Copying the savedvariables file seems to be most common. However, it won't edit out the duplicates. I think most people usually replace their data with the DBs. I thought I saw a script on these forums somewheres to merge them though.
The way that I think is best is to right a simple function that imports it for you and checks to see if it exists before it adds it. I had something like this written a few minutes ago for Quest Objectives (then my computer crashed) and... I figure I'll rewrite it again tomorrow or the next day.
Alternately, you can copy/paste if you do it to the right spots. I recommend against this for the reasons you stated above and because it's pretty easy to paste stuff in the wrong spot.