The important thing to note is that You do the profile and the refine (play loud chords etc). Then you have a few adjustments available that can make that profile sound even better than the amp.
In the AMP section you want to pay attention to the DEFINITION control. This will add/remove some of the bass from the signal BEFORE it goes into the amp section. Low settings for Clean Fender type bass and High for tight high gain amps. This should be the first thing to adjust.
If you are doing clean amps you will want to add a little compression to even out the dynamics of the amp. This tries not to color the sound. Use the Compressor stomp to add some color (also useful for clean and slightly dirty). Use the Michael Britt settings (all dials on 12-1 o'clock) and adjust the mix to taste.
I usually like to play around with the AMP CLARITY setting next to remove some hair on the sound and then use the AMP MIX to add a little clean sound to fatten up. Use small amounts of mix.
Then you can adjust the CABINET hi/low and character to put the amps fizz in the right frequency range and make your speaker sound larger or smaller. Then I tweak the CHARACTER if the sound sounds too muffled or it in a tube. Lower to get rid of frequency effects of cab/mic.
Then add a TREBLE BOOSTER after the amp if you want some extra presence and boost. Mix at a low value (5-20%) and adjust tone to get the presence you want.
Add a graphic or studio EQ in the first stomp slot and you can dial in the sound even more. This tweaks what hits your amp front end so you can adjust it to tweak the pickup sound or boost the mids to get thicker gain from the amp.
You should now have a sound that is even better than the real amp and you have not even played with effects, post amp EQ, etc
Cheers