What's the different between two rotamer library?
If I use dun08 instead of rosetta default library, can I get more accurate side-chain packing result?
Dun08 is more recent and better in many ways. In particular, it has been smoothened so that the energy changes more smoothly as the rotamer identity changes.
The default scorefunctions have not all been rebalanced properly to work with Dun08, so you might or might not get better results if you swap Dun08 into a protocol using scorefunctions with Dun02.