Today I tried some ways to convert to SD material.

The best sharpness and quality was aquired when just importing the footage into a DVCPRO50 sequence. However the movement and thin lines in the image was flickering! The source was 1080 50i

Tried importing through the SD port on the decklink to 10bit uncompressed as well but the sharpness wasn't the same as the direct import. The movement however was super smooth.

How do I best import from the EX1 to a sequence with DV50 material?

I had the same flickering effect.
Managed to solve the problem. However I'm not sure how to give you the proper explanation as my FCP6 is in french.
Lets try...
The path must be something like this:
> "Effects">"video filters">"video">"shift fields" (+1)
apply the effect ...and render.

If the above doesn't work, you might try adding a little gaussian blur. I know it sounds counterintuitive, but SD video can't handle the fine detail captured in a high def image. The slight blur reduces the chance of "line twitter" which is probably part of your problem.