mixing effects when joining videos

Hi,

what is the best way to go about mixing effects when joining two
videos, like crossfading?

Once I have the individual images as numpy arrays, the mixing itself
is the easy part (I'll just use numpy + scipy for that, or any other
python lib). However, it's not clear to me how (and especially when)
to handle decoding and encoding properly.

So lets say I create a video tutorial (screencast) and I have 3 ogv
files. Now I want to join them --- so if I want some mixing effect,
one way is to decode them, mix them + join them and then encode it as
one video. I can do that already. But every decoding and encoding
makes the image a little worse (am I right?), so what is the usual
practise?

Another question is about frame rate --- (e.g. one frame rate for my
web camera stuff and another for the screencast) I read that theora
can join them, so that's fine, but if I want some mixing effects? And
if I want to upload to youtube --- they will convert it to some other
format, will it still work? So I guess it's the best to use one frame
rate for everything, then I am free to mix it anyway I want. I found
several programs on the net, that can do frame rate conversion (I
guess some interpolation, so that it looks good). So it seems to me
that everything is possible, so my questions are mostly what the best
way is to go about it.

Ondrej