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If you use Flex Builder 3 in its standalone configuration you can definitely install it and not interfere with Flex Builder 2. If you use the Eclipse plugin you'll need a separate install of Eclipse or will need to use the standalone build.
Related: Is it possible to use Flex Builder 3 against Flex SDK 2? I am hoping to leverage the refactoring + memory profiling abilities of the new version.
Yes! You can use Flex 2 with the new Flex 3 Flex Builder taking advantage of the new multiple-SDK feature. Here is the description of the feature:
In summary, you can have multiple Flex SDK's installed and target particular projects for these sdks. So, you can take your existing projects and continue to target Flex 2.0.1. At the same time, you can point any new projects to the Flex 3 sdk.