Hi,
I will try to answer to these questions:
>>If I have .net 3.5 sp1 - do I just click on one of those entries and click manage this software. ?
You can do it if you want to create software product and then add package from Software Product UI or you can just double click to the software component under Newly Discovered Software -> go to Packages tab -> select Add Package (checking Automatically generate command lines option).
>>what happens to the other entries ?
Nothing. If they are actually the same, then you can merge them to one Software Resource using Resolve Duplicated Software Resources option.
>>What are the benefits (if any) of doing this rather than just importing a package from new ?
The benefit here is that in some cases imported software resource will have different combination of Name, Company and Version items comparing to discovered software resource and as a result you will have duplicates in Software Catalog which you will need to resolve manually.
Thanks,
Andrew.