I used enable this support manually i.e. opening up the web.config file and making the necessary changes. I felt that this was a safer way to ensure that nothing went wrong. Recently though I have found a much better way to do this – Jan Tielens has a blog post on how to enable .NET 3.5 in SharePoint by using Visual Studio to modify the web.config for you, it works very well and is really quick to do.
You can find his blog post here –
Thanks Jan! (@jantielens on Twitter)