"De-Interlace" the image make smooth.Try it!

The second question is, what format should i shoot with on my EX1R, as it allows me 1920, 1080 or 720, keeping in mind that i will have a timeline with shots from both cameras on it, which means that the timeline will have at least 50% of 1080 footage shot with my hdr fx1000.

The third and final question is, if i want to do some super slow motion shots with twixtor, what is the best format i should shoot with?

Thus, if you shoot 1080P on the 1000, to keep things simply, you should shoot the same on the EX1. Now, I'm not at ALL familiar with either camera, but the convention is the same and I think my logic is sound for keeping your footage and editing efforts simple. If both shoot 1080i and you want to shoot that, keep them the same.

And yeah i understand about not having to de interlace the progressice scan footage, its just ive been told that the progressive scan footage on my cameras isn't really progressive footage as such. its just interlaced footage modified to create a progressive look? Is this correct?

12p (0.5x 24p) will definitely look stuttery, more so than 30p (0.5x 60p) if you're shooting 60p. There's no software that will magically transform interlaced footage as if it was shot in progressive.

Doesn't de-interlacing interleaced footage make it progressive? Also i ment if there was any software such as Twixtor that allow you too slow things down, as im using it but still cant get the crisp, clean and smooth slow motion that im after.

In a simplified terms (and I'm certainly NOT a genius for writing the engineer-level deep technological stuff) yes, it could be said that de-interlacing essentially creates "progressive" footage. I also know there's more to it than that, but like I said ... beyond my pay scale/knowledge :-)

If it were me, given your choices, I'd shoot everything interlaced (since that's looking smoother to you when slowed down), do the de-interlacing if it seems to help, and the stuff I want to super slo-mo I'd shoot at whatever the fastest shutter speed your cameras offer. I'm not intimately familiar with either of your models, or Sony in general. Sorry.

Of course that (faster shutter speeds) might introduce other "issues" due to available light, etc. I hope some of the higher level tech heads here will respond and help get you the answers using your currently available units to acquire the smoothness you want in your super slow motion work.