Thanks to both of you. After thinking about this further, I think I would rather let synaptic install the repo version of ffmpeg for general use, and keep the built from source binary somewhere out of the path for just for converting the files from my camcorder. I'll probably create a batch file for the conversions so referencing the out of path version won't create a hassle.
Here is what I have done. Everything seems to work fine, so hopefully I haven't created a mess in my system. I found the installed from source binary of ffmpeg in /usr/local/bin, and moved the binary to an out of path folder. Then I installed ffmpeg via synaptic. This put the binary in /usr/bin/. For some reason at this point when I ran ffmpeg -version, it threw an error message: "bash: /usr/local/bin/ffmpeg: No such file or directory". I'm not sure why it did this, since both folders are in my PATH. To get around this I created a link in the /usr/local/bin folder to the version in /usr/bin.
This seems to work fine. Do you see any problems I might have created in doing this?