What format to export if using third-party encoder?

I've read the manual on this but I still don't think I've got a full grasp yet on exporting a reference movie. I wonder if someone can help enlighten me.
Does exporting a movie using the Using QuickTime Conversion... option, and then selecting an encoder (say, H.264) produce a "reference movie"? If so, then what's the diff. btw the above and using the export to QuickTime Movie... option (not self-contained)?
The reason I'm asking is because I'm trying to determine what export format I should be using if I'm ultimately going to use a third-party encoder that's not listed in the FCE standard encoding options? (I.e., ON2 VP6 encoder to encode my movie to Flash.)
Thanks in advance.
macbook pro   Mac OS X (10.4.7)   2.16 GHz, 1.0 GB RAM, 100 GB HD, Panasonic AG-DVC30

Thanks, Tom.
I'm almost there... you answered the first question and I think I can bridge it to the other.
Based on your post, I'm now clear on the Quicktime Conversion option as generating a self-contained movie file. Thanks.
On the second part, I'm using an On2 product that doesn't list in the format drop-down list. (Unless I'm missing it entirely.) I think the one you're referring to may be the On2 Flix Exporter package. However, I'm using On2 Flix Pro, which is a standalone. But, I'm now in danger of digressing from topic...
...Just to clarify my understanding, what I glean from your post is that if I were to use a third-party codec that doesn't appear in the drop-down format list, then I should:
1. Export to QuickTime Movie;
2. Un-check "self-contained" (thereby making it a reference movie);
3. Then use the reference movie file as an entering parameter for the third-party codec.
Right?

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