Although the MixControl options are pretty thorough what I do when recording to get a good balance is use busses within Sonar to adjust things as I track. I set the Scarlett input trim (or now my mixer via the line ins on the Scarlett) so that the track within Sonar is getting a good signal and then adjust things as needed in Sonar's bus section.
So basically every instrument gets a bus (drums, bass guitar, vocals, any synths all have a bus). I group all the related tracks to their own bus, (all drums to a bus, all rhythm guits to a bus, etc...). The track levels are set so their busses are all getting a decent mix/level.
I also create a Pre-Master bus that everything gets routed to before the master and then that premaster gets routed to the master (I do this for various reasons but I won't get into that but one factor pertains to this).
So... if I am tracking and need to hear the input of the track being recorded or any other instrument I just turn up/turn down the relevant buss. If I do not want to mess with the mix of the already tracked busses what I can do is send the input of the new track being recorded straight to the Master buss and simply adjust the Pre-Master buss level to where it needs to be in relation to the new track being recorded (it is very easy to just put that Pre-Master bus level back to where it was as opposed to readjusting all the other busses).
Once a decent mix between the Pre-Master buss and the new track is set then I can crank up the headphone level knob on the interface as needed.
You have to remember that once you have your input trim set on the hardware THAT is the level being recorded no matter what level the track or buss faders are in Sonar (you can have the track muted and it will still record if you have it armed... I did this yesterday to test it actually).
So yeah... a headphone amplifier is a handy device to have but your 6i6 actually has TWO of them from what I just read. It is one of the most useful features on the Scarlett series. When I bought my 18i6 I was freaking out before I got it because I thought I would have to buy a separate headphone/monitor controller. When it showed up I saw I had individual knobs for both the mains and the headphone jack. SWEET!!!
Anyway... you will likely find uses for your new headphone thingie (they are extremely useful) but there is more than one way to skin the proverbial feline... especially when you are using a Focusrite product with Sonar.
Cheers.