@BAFelton
Damn, why didn't you ask these questions 4 months ago, when this process was fresh in my mind
Anyways, I will do my best to try and get you on the right path. I don't have my original video files handy, so I'm just going to give you the info from the ones I'm currently using. I also hope you already have DAPHNE up and running, as this information is just to help these clips run better. As getting DAPHNE running from sctratch is another ball of wax altogether.
Once you run SUPER and add your video file to the conversion box, you can double left click on the file to get a detail of that clip. If I remember correctly, I would keep the framrate the same as the original along with the aspect ratio. I would only ever change the video scale size, and the bitrate. I believe the video size for AstronBelt needs to be manually done for 512x480(aspect 4:3), and I would pick a bitrate around 2000(a number higher or lower, as you can't set a specific 2000).
The encoder I think I kept on MEncoder or FFmpeg, I can't remember for sure, I played with differant options, but I don't think anything really changed in that area. I also tried the High Quality option as well, and I don't remember if that does anything special either, just leave it off for now.
The output container should be "MPG" and the video code should be "MPEG-II". Lower down in the audio box, just pick "disable audio" as it is not needed(as normally your video clips should be audio-less anyway unless you are making your own clips form DL sources). Now when I say it is not needed, normally any daphne video clips should also have a seperate audio OGG file included. Even though you change the video around a bit, the original audio should still work fine with the new clip.
Now for stream clip, this is for "Demux"-ing the file. DAPHNE needs the audio and video to be in 2 seperate files, so once you change your bitrate and such, it makes the file appear to be a certain way which I believe looks like audio is included. So you use this program to seperate your new vido clip to a file that no longer includes audio. Now you may be thinking, I disabled audio so why do I need to do this? I have no idea, it just makes Daphne now use use your new video clip as it should. Now, if you have converted a dvd image over, then you would use this method to seperate out your audio clip as well, as you wouldn't already have that since you are making your own audio and video from sctatch(this was to much work for me, and it can only be used for DL, SA, and DL2).
I hope this helps, as this information was no longer fresh to me, but I think I did a fairly good job to remember. You can always play with the settings in SUPER to try and improve how well your video clips run with DAPHNE. I personally just followed the recomendations of other users in regards to bit rate & screen resolution. Once The games ran for me, I didn't bother to try to improve performance or anything else, but you can if you have the time or the desire. If you have any other problems, feel free to ask and I'll do my best to answer with a worhtwhile answer.
Chris