Welcome to the forum NASABlue.
As with anything new, or new to you, there will be a learning curve associated with it. In this case, you are faced with learning to tune and learning to use the tools to tune. Getting started can be quite overwhelming at times.
Rather than "when all else fails, RTFM", I would highly recommend you make the time to read thru the Scan and Tune tool manuals and tutorials to help you become more familiar with your new tools. Interactive tutorials are available at www.efilive.com.
I would also suggest that as you work your way thru becoming familiar with your tools that you post and search the forum for any questions you may have. There are litterally hundreds of folks here that are more than willing to help you along the way. All that anyone asks of you is to be curtious and when the time is right, help the next guy along.
Just remember, TAKE YOUR TIME, read, ask questions, read, ask questions, read, ask questions, take a baby step, then read, and ask more questions.
They didn't create EFI over night and no one ever learned to tune overnight.