I'm working at a production house where we use a SDX-900 DVCPRO50 camera.

Our projects are based on this format.
On some projects i use my EX1, but we can't seem to figure out what I should shoot in to get the best results when using this footage in an DV50 SD Lower field timeline.

The progressive material of course have a choppy look on panning shots..
Should I shoot HQ50i? Or even HDV?

Any thoughts?

Are you shooting at 1080p25 or 720p25? Try shooting at 720p50. I'm mentioning this because you noted in particular the pans look choppy.

Of course if your camera work is carefully geared for the frame rate, pans shouldn't look choppy. Do the pans look choppy when played back in their native resolution? If not, then the issue might be how your NLE is mixing formats rather than an issue with the source video.