The Most Important Question: how slow is slow? Half the normal speed? So slow you can see a bullet passing through an apple?
It makes a difference.
> 1. What would you recommend me to to, Edit the clips with effects/cc/slowmo and so on in after effects clip by clip and then sync and put all together in premiere pro? Or is it any smoother way to do it?
That depends on a lot of factors. I'm going to presume that you are going to shoot way more video than you need. If this is so, then you don't want to process a bunch of footage in After Effects that you're not going to need. That's why you should do your rough cut in Premiere Pro and then just send the little pieces over to After Effects that you're actually using.
> 2. Of cource I want the maximum quality and my question is what I should use for settings. I got a pretty beast computer so I dont care really to keep it to a small file.(Its going on to youtube btw). Is there any codec I should download or anything? uncompressed is the best quality I guess but it should different uncompressed codecs?
For your final render, you should be going through Adobe Media Encoder and using the built-in YouTube encoding presets.
For your intermediate files, you have a lot of choices. Personally, I use QuickTime movies with the PNG codec as intermediate files between the NLE (Premiere Pro) and the compositing application (After Effects). ProRes 4444 is another adequate option, even though it's slightly lossy. There are many other choices. Just don't use a format that compresses a lot for your intermediate files---e.g., don't use H.264.
> 3. Will I get less quality if I first render a clip in after effects and when I got all the clips done in premiere and rendering everything there?
No. The reasons for chooisng one workflow over another are for efficiency, not for quality.
> I will be using twixtor.
Why? What's wrong with the Timewarp effect and time remapping built into After Effects?