As much as I hate video guides, this one shows you how to setup Aurora as the default dashboard.
I personally prefer the stock dashboard and just install games as GOD (Game-On-Demand) titles instead of using a custom dashboard and game folders, but you're free to choose whichever.
In DashLaunch (the same app you set the default dashboard with), plugins are to be setup in it. This meaning stealth plugins if it's specified in their install process.
I've been using Proto (stealth plugin) since it's free, for about 2 weeks now and I haven't gotten banned yet. Your mileage may vary.
In my opinion, FATXplorer is better than moving files via FTP since it's a direct SATA connection (plug the hard drive into the computer) without relying on slow and possibly flaky networking. FATXplorer is a paid program, but has a 7-day trial period although with some limited functions (files can still be moved around and installed in trial mode).
If you have a hard drive with no security sector (meaning you popped in a regular hard drive and formatted it with the serial number prompt in the dashboard), some other programs meant for modifying the hard drive contents may not work. I ran into this problem using an 80GB hard drive. Party Buffalo, Xplorer360 Extreme2 and that Datel program did not work for me. Again, your experience may differ than mine.