Do you mean different parts of one complete model having different amounts of infill, or one model in parts, with each part having a different infill?
Infill can be set in the slic3r settings when you print, so broadly speaking you could print one part of the model, set the infill to 80%, then print another part and set the infill to 20%. Infill is not normally set in the original model itself.
If possible, the best solution is to split the model, and just set the infill as you print. Infill is all automatically generated, so it's not that easy to set it differently in different parts of the model. (I'm sure that someone can prove me wrong on this, but it's not something I know how to do.)
If you want to give a part extra strength, and you don't want to split it, you can always embed a support inside the model, as long as it's still manifold. It's tricky to do (for me!) but the slicing software then treats that bit like another surface and prints layers around it.
As an example, this vacuum pump: http://www.thingiverse.com/thing:29623
The part that connects to the hose, I think, needs higher infill. The model is printed in parts anyway, so that part could be put in a separate STL file, and printed with 100% infill.