I'm not sure if this is the correct place to put this, but I just wanted to share something that may or may not be well known.
Whenever I see composites done for live-action and/or CGI scenes that are combined with Stop-Motion, I notice that it doesn't blend in well. Now I know I'm nowhere near being an experienced animator that can give good advice, but for those who want to know a little trick that I've used for all my composites, it's something called the diffusion filter. It's great for blending in multiple composites. Again, many of you might already know this technique, I just wanted to offer a tip or two.
What software are you using? I was thinking that maybe there was a VDF diffusion filter for Virtual Dub or Wax 2.0 but I couldn't find anything. Sounds like a good idea if your software supports such a filter.
When I first tried, I used a plugin for Virtual Dub. The result was disappointing. When I recently combined rendered CGI frames with live action, I used a diffusion filter on GIMP 2.8 (One that I've been using for quite a while now). The only frustrating thing was that I had to do this to every single frame.
But hey, it worked!
The best software for doing compositing to an entire video file is After Effects. It has a Diffusion filter plugin.