If you are working in AE you are in the safe house, make sure you are in 32bits before any manipulation. You could ask Sarreesh this question because it seems that he uses A.E and I'm sure he would be able to guide you within A.E. I'm using Nuke and unfortunatly cannot give you any A.E tip, but what I'm sure is that if you are in AE, you'll be able to obtain great results. I would maybe re-orientate your question to "neat within A.E", something like that, that way you'll have answers from the people using the same software.
Sorry for the shortcuts. I.S stands for image sequence. Compo = compositing, like A.E.
In general, compositing software like After effects, Nuke, like image sequences. Most effects artists work on those programs in image sequences. It's stable and got the datas to work with without degradations.
If your software allows it (and I think A.E does), working for example in open EXR would be very good because they ocupate less space than tiffs. http://www.openexr.com/
It's the prefered format here because of that. But on the other-hand, tiff will be a more flexible way because if you are not happy with the Neat results, you can always go to C1. With open EXR you'll only have the Photoshop option as I doubt Capture One supports open EXR (but Photoshop does).
Ps: I think that the FS700 is a great camera. Probably the best within the 8 bits range with maybe the Pana AF100 (that would need a serious up-grade), certainly way better tan dslrs. In fact, the need for more robust artillery appears only in certain situations and 70% of the time it would deliver great footage.
However, when real manipulations need to be done, like compositing, perfect keyings, noise removal (depending very much on how bad is the original), the format delivered by those cameras is too short and degrades too early. So a convertion has to be done. The convertion do not add any datas at all, but avoid loosing more.
It's like you got a jpeg and want to do heavy retouching with it. You're going to convert that jpeg into a PS, Tiff etc...format. No datas are added, but no more datas will be lost during the manipulations and you can do families (tiff to tiff etc...). Instead, compressed formats loose each time a new generation is generated.
Unfortunatly, Raw video is not yet democratized enough.