Yes, a .qc file is generally only for that model. With other words, whatever settings and stuff is in the .qc file will get compiled into the .md3 later on and will only be applied to that model.
Here is a example .qc file for the flags I made way back. Where I specified what texture should be used for what part of the model. I had 4 different separated parts of the model where each could use it's own UV layout and own texture for it (however I ended up using one same combined layout I believe). But you could use several overlapping UV layouts if you so choose.
Anyway, I do not know all the code which could be used in a .qc-file but I didn't really need to know it all anyway. If you wish you could try to study up on it.
There is also the possibility of defining how many frames an animation is and stuff, however it didn't really work well for me for some reason. I think my Milkshape or my approach was off.
This is one of the reasons why I switched to dpmodel (also Milkshape costs money so you'd save those pennies -_^).
Dpmodel can be found here:
http://icculus.org/twilight/darkplaces/ ... 2beta1.zip
However, dpmodel is updated all the time and you can go to this link to check the different versions and stuff:
http://icculus.org/twilight/darkplaces/files/?M=D
There is a readme and an example of how to convert your model into .md3. But keep in mind, in order to do that you'd need an .smd file of the model first. I don't know if more, and if so which ones, file extensions are supported. Someone would have to clarify that.
Good luck!