How do you analyze and align phase between two audio tracks in SONAR.  There are some WAVES plugins (in phase) but I had huge problems with drum replacement and micing and really only knew how to hit the phase reverse button , which seemed to help but what do the reeeel pros do?

You can zoom in tight on two wave forms and drag one of them to get them more aligned. Make sure snap to grid is turned off.
 
Rocky

I am OK at that, how do I check the phase? is there a phase checker? I thought I saw something like that somewhere?  like even though the transients and wavs are perfectly alligned they can be out of phase I think.

The important thing to remember here is that there is no such thing as "correct phase". In any given pair (or more) of mics on a single source, different components of the signal will have different phase relationships.
 
To give a simple example, take top and bottom snare mics. You might alight the transient section really tightly to get a good crack there, but then find that the decay portion of the signals don't seem to align as well. You could actively choose to have less alignment in the transients than in the decay section. It's really a question of choosing your compromises according to what you're trying to achieve.
 
This stuff is fun (and even worthwhile) to mess around with, but there's no one correct way of doing it.

There is an included Sonitus plugin called "Sonitus Phase" that helps identify and correct phase issues. I don't fully understand it or exactly how you'd set it up in a top/bot snare set up but it can be found by "Insert Audio FX > DX > Sonitus > Phase.
 
Basically there is a meter that shows you how out of phase something is and a fader you adjust to correct the phase. I guess in your situation you'd create a bus just for the top and bottom snare tracks to be sent to, insert the Phase plug on the bus, watch the meter then adjust as needed.
 
There also seems to be a stereo width fader as well but I'm not sure exactly if that's what it does. Anyway... just check the F1 file on it and it should explain it better then my hamfisted blathering here.
 
Cheers.

Waves Paz and the T-Racks metering suite have phase meters. I have been using Slate Digital Trigger for drum replacement and phase issues are non-existent with close mics. I make sure I get the overheads right during tracking. XY is fool proof for overheads.
 
Rocky

I think by:
"hit the phase reverse button"
you mean you inverted the polarity.
 
The Voxengo PHA-979 might be what you are looking for (I have used this plug-in):
 
http://www.voxengo.com/product/pha979/
 
Blue Cat's Oscilloscope Multi might help you analyze your tracks (I have not used this plug-in but I like Blue Cat's plugs as I have used their eq)
 
http://www.bluecataudio.com/Products/Product_OscilloscopeMulti/

Yeah I checked them out that bluecat looks awesome, compare two tracks.  Thanks too John T.  I see that when saying phase I am really talking about timing, but the end result in the ears is what I want to play with, especially the rattle and the top side of a snare recording.   The bluecat tool looks perfect but the demo video is showing how to align snare to the overheads (3 milliseconds later).  Would we "want" to do that I wonder?  Do most professionals NOT leave the delay between the close mics and the XY overheads?  hmmmm. http://www.bluecataudio.com/Products/Product_OscilloscopeMulti/
as an aside is the dude making this video toasted or what?
 
Also how do you pan your XY in the mix? I found I really have to bank them to get a good stereo spread. like at least 80% full pan

papacucku
I thought I saw something like that somewhere?  like even though the transients and wavs are perfectly alligned they can be out of phase I think.

If the transients are "perfectly aligned", then they are, by definition, in-phase.
 
You cannot ever truly get two microphones completely in phase for all frequencies, though, as each frequency has its own phase relationship due to different wavelengths. Because it's physically impossible there is also no plugin that can do it, either.
 
You can adjust the phase relationships between the snare and overhead microphones by ear the same way you tweak dual mikes on a guitar cabinet. You're always going to get some cancellations, but some phase cancellations are less obnoxious than others so some experimentation is required. There is no set formula, and it'll always be a compromise (don't forget the tom/kick/hat mikes).
 
And you're right about the pro's not ignoring this, but they usually resolve it with mike placement rather than by editing the recorded tracks later. That's one reason you see permanently miked-up kits in studios - they get it all just so and then don't mess with it again.
 
You can also see why some hard-core old-schoolers insist on using a minimum number of microphones on drums, some preferring a single mike up high and another on the kick and that's it. It does simplify things greatly.

papacucku
 
Also how do you pan your XY in the mix? I found I really have to bank them to get a good stereo spread. like at least 80% full pan

XY is intended to be fully panned (as far as I know). It's supposed to provide a full stereo image.
 
I am not a pro but yeah... that's kind of the point of XY.