MCC is a great hands-on tuning tool. You can view the differences between tunes and combine that with timing calculation theory, etc. Make little changes here and there, then move up to building entire timing tables.
One great place to start is on the transmission tune. It is amazing the difference in drivability on one truck vs. another with the same exact tune. Differences in weight, gearing, tire size/weight, etc. combine for a very different driving experience between two vastly dissimilar trucks.
But to be able to get the shifting dialed in exactly how you want it and feel like it "should have come from the factory like this" is just the cat's meow, and you don't have to worry about tearing up the engine.
Not that you're going to tear up the engine on a stock-ish 6.7 with a tune unless you just plain TRY to