I prefer to export a QT reference file. This avoids tying up FCP and compressor. Because FCP renders each frame of video while exporting straight to compressor, you can't use FCP until the export is complete. Depending on the length of your sequence, and the codec/quality settings you're using, this could take a while.
There is no difference in quality with one exception: FCP projects with Motion generated animation will yield higher quality by Exporting using Compressor. I have not tried to find the differences and it makes no sense to me as to why it would have anything to do with quality, it's just what I've heard.
Have you had a look at the FCP manual? It typically has just about all the answers to these types of questions.
If you are able to find solid answers as to which way is better for this reason or that, by all means, let us know.