.MTS transfer headache, and sequence setting suggestion needed

Hello forum users...
I am trying to edit a sequence with scenes captured on a variety of recording devices (SONY AVCHD, GoPro, and ScreenFlow screen capture)...It's a headache enough to try and get them all to match up for size and compression. I bought emicsoft's conversion software and converted the original .MTS files from a folder on my desktop into .MOV files. FCP could read them (although I sometimes get a red bar on the timeline when I bring them in...), but when reviewing the original .MTS compared to the new .MOV I noticed a drop in quality.
I researched on the forums and saw how people were suggesting to convert the .MTS through the "Log and Transfer" feature... I tried this and was given this message: "00009.MTS" has invalid directory structure. Please choose a folder whose directory structure matches the supported media.
...so i researched further, and saw I needed to drop the file into Final Cut Pro>Capture scratch folder, which I have done, but when I try to bring the file into the Log and Transfer window I still get an error message, or if I try and just drag and drop, the icon for the original .MTS is grayed out.
...I kinda have steam coming out of my ears about now, so any suggestions would be extremely grateful...
P.S. while I have your attention, any suggestions on what "sequence setting" I need to choose if I am using these converted .MTS files in addition with other files that are mpeg4 (1440x1080) and DVNTSC (1920x1080)???????
THANKS!THANKS!THANKS!!!!
-O
Message was edited by: ufoliver2

I converted to a .MOV file (mpeg4) because I thought that was the best option I had using emicsoft's conversion software...you practically need a machete to get through all the options. Unfortunately Quicktime prores isn't on the list...
I got the MPEG Stream clip file, but when I open the .mts files I get a message: "unrecognized file type", so I got the Clipwrap program trial, and it looks like I can just convert .mts to prores 422 from there..
Which I did, and imported into FCP. Opened and played beautifully...it asked if I wanted to set the sequence to match the clip, I said yes. But then I brought in my .mov files (captured from SCREENFLOW, and also shot on the GoPro camera -at a different frame size), and imported them into the time line... the screenflow one became really small and went to the upper left corner and the rest of the canvas screen was some pink and green posterized version of the clip, and then when i brought in the gopro it couldn't play ("unrendered").
the screenflow.mov wouldn't open in Clipwrap, so I went into streamclip to convert to 422, and converted the gopro .mov also to 422.
I went back and imported all 3 different file types... the MTS converted to 422 played beautifully, the screenflow converted to 422 played beautifully, the gopro converted to 422 came up UNRENDERED in the timeline with a red bar across...
...now the gopro shoots at a different frame size..its not full letterbox, it come up more like a square..1280x960
I AM SO CLOSE...75% there... I THANK YOU ALL FOR YOUR HELP!
BUT, last issue to solve (for the time being...;) ...how can i get the 1280x960 clip to show up rendered?? I ran it thru streamclip and converted to 422, so that isn't the issue...
THANKS!THANKS
-O

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