Q: How come it takes longer to transcode files?

Project folders? What version are you using?

They're libraries. They content your events and projects.

Do you have Prevent App Nap checked on in Finder info?

You want prevent checked on.

YOUR SECOND QUESTION:

> Ideally, you should move Libraries to another drive within FCPX. However, those 4 Purple Star Icons... those are your Libraries ... as Tom mentioned.

http://support.apple.com/kb/HT5958

> You can copy/move those from one drive to another as those Libraries contain all of your files. They'll contain your original media ONLY IF FCPX managed your media and copied the clips. If you just pointed clips and videos from another folder (leave files in place option when importing), you'll need to make sure that those go along with your copying/moving. Then you'll have to relink them later.

> Post again if you need more help with that part. Now with this new Library structure in 10.1, it's my opinion to have FCPX "copy files" for you when importing.

You don't import it. Just double-click the library in the Finder to launch it.