I'll shed a little light on this subject as far as the latency adjustment goes. In my opinion, everyone should do a manual adjustment because if you do an actual test, you WILL indeed find out that your soundcard SHOULD be aligned to Sonar but isn't.
There was a member on this forum...Eric Beam (RhythmnMind or something) that created a test file showing us how to test our soundcards as well as how to tweak them to work in Sonar. Every machine I have tested this on that I use here, has needed a manual offset adjustment. I would always wonder why some of my tracks weren't quite right over the years.
One thing I pride myself on, is my timing. I'd put myself up against a metronome anyday and come so close, no one would be able to tell. The day I learned about this test from Eric and actually did it, was the day I never had an issue with my files being messed up again. Trust me...those that think you don't need to do this test, will be astounded when you find out how much you need to adjust your cards.
The key is to run a test file in Sonar. I do not believe the test file you use matters, but preferably a mono test file. Actually, here is the one Eric gave us...so use this.
https://dl.dropbox.com/u/4909348/interface%20timing%20test%20file%20%40%2048k.wav Set your latency for as low as you normally do to record. Then, take that file that you've imported, and record it into itself. Meaning, take the out of that track where the imported wave is, and run it into the in. So if you use 1/2 for your main outs, run one of them into INPUT 1. Arm the track, and record it. Do a few test runs to try and get the levels of your recording the same as the test file you use. If you zoom in, you will see just how off Sonar is from your soundcard. As I said, not a single machine I own running Sonar has passed this test without a tweak.
From there, go into your nudge settings and set it for "Samples". Hi-lite the track you recorded, zoom in tight and nudge it in the direction you need to go to make it be perfectly in line with the imported wave file. As you do this, count each time you press a nudge direction. When you are done nudging, take the number you come up with and input it into Sonar's manual latency adjustment. If you had to move your clip to the right, input a negative number. If you had to move your clip to the left because it was recording late, input a positive number. Still allow the check-box to remain for Sonar to take care of it for you, but put your number in.
Then, delete the wave file you recorded and record another one now that you have put that number in your manual latency box. The wave file, when zoomed in, should be identical to the test file you used timing wise. That's all there is to it. Try it, you'll see how off your stuff really is.
-Danny
Edited due to positive and negative advice being backwards....fixed!