Root Two post-root questions

[Grimshak]

First, I've already rooted and tried several roms, so far my favorite is NexBeast, but I'm about to try out the Nex-themed version of BB froyo. Anyways, two quick questions.

1. How do I run all these rom-specific scripts mentioned in new rom releases. And do I risk damaging anything if I have back ups through Nandroid?

2. I'm interested in replacing the default boot animation. What are the risks (if any), and how do I back up the default boot animation if needed?

Thanks!