Let's say I have a dry bass signal on a track, and I want to send a little of it to a bus that has a bass amp on to mix a little grunge into it. Is it customary to flip the phase on the send track? I'm a little in the dark regarding issues of phase. 
 
The reason I ask is because if I do the above with Mark Studio on the amp bus, I get a drastically different sound if I flip the phase switch on the amp. Also, if I use the same technique but with the Aphex aural exciter, sometimes the results sound a little phasey. 
 
One weird thing I've noticed doing this technique, is that if I loop a section of the track in question when I first fire up the project, and play back that loop, the first iteration of the loop will sound normal. But when it returns to the start for the second iteration, the phased effect begins, and remains for the duration of that session (i.e. until I close the project and reload it). Not sure how significant this is or if it's just another one of those oddities that happens when looping in Sonar. 

I wish I knew what you were asking. 

Well put it this way: If I just have Mark Studio on a bass track (not a send bus), flipping the phase button (in Mark Bass) has no effect. But if I put it on a send bus and mix it in with the dry bass track, flipping the phase button makes a very drastic change to the sound. I'm just trying to get a better idea of what's going on with that. 

Is it a mono track or stereo track?

In the case of the bass track, yes both the track and the bus are mono. I forgot to mention that they are both then output to another bus (also mono) for compression and EQ.

There should be no phase on a mono track. I believe you are seeing (or hearing) an artifact of the plugin. 

Hi Sharke,
I'm not sure what John is referring to regarding stereo and mono, but the phase button just flips the positive and negative aspects of the waveform in a track. Easiest way to see this is to take a track with some audio on it, hit the phase button, bounce to a new track and zoom in. You'll get something like the following, where the track on top (in green) is the original and the one on bottom (orange) is the new, phase reversed, track. Notice how every time the waveform goes up on the top track it goes down on the bottom:
 


If I play those two tracks separately they likely sound the same, but if I play them simultaneously the result will be silence...summing two identical tracks whose phase are exactly reversed results in silence. This is the crux of null testing (a method of finding out if two tracks are the same).
 
The phase button is most commonly used when handling multi-mic'd instruments. For example, when dealing with a top snare mic and a bottom snare mic one of them will pretty much always need to have it's phase flipped.
 
So in your application when you have a single track, with or without a bass amp, and flip the phase you end up not hearing a difference. But if you have a second track that you are playing along with the first track and you flip the phase on one (and only one) of them, you'll hear a big difference. The two are being summed and thus you're hearing the results of an additive process. 
 
It's certainly not required/customary to flip the phase when re-amping like that, at least not the way it is with snare drum mics, but it's absolutely something you can try. Sometimes an amp or plugin will affect the sound in a way that brings it out of phase with the original and you'll want to hit that button. Sometimes you'll want to do it to intentionally bring two tracks out of phase with one another, just because it sounds good. Sometimes you'll even want to flip the phase on only one channel of a stereo recording because it changes the sound in particular ways (that's actually a kinda common technique but be careful, it can cause mono compatibility problems). The "required rules" regarding phase, such as they are, are really only for multi mic applications and testing. Anything else is just creative use.
 
Good luck,
Dean

If you flip the phase on a mono track there will be no change in the sound. Phase comes into play with stereo. 

John, Phase comes into play on mono summing... not just stereo sound. I know you know this, so I'm stating it for clarity for others.
 
If you take a track and
1. route it to a bus,
2. send it to a different bus on which
  a - you add distortion through an amp sim plugin
  b - you further distort through a phase flip (I think this phase flip you were doing was on the amp sim not using something trying to be 100% clean flip like a channel tools phase flip or a Vintage Compressor phase flip).
  c - route output to the same bus as the original track
 
You will get lots of interesting effects. You will probably get a good amount of cancellation of the original signal which should be strong in both the original track and the phase flipped track. So, lots of the original sound will cancel and you will be left with the differences of the two tracks.
 
I like Razorwit's suggestion of bouncing so you can see the wave forms and compare.
 
You can use mono phase flipping to do zero sum cancellation to see what impact certain FX are having. For example, if you want to hear the effect of a console emulator turned up really loudly, you could clone a track and phase flip one of the two tracks, put a console emulator on one of the two tracks and bounce to tracks. Most of the original signal should cancel out. Now, normalize the results and you will have an example of console emulation sound generated on that particular track.

Hi John,
Respectfully, that's just not the case. Phase matters every time two tracks are summed, stereo and mono have nothing to do with it. This is why you reverse the phase on one of the mics when micing a snare top and bottom, even though they are mono tracks. This is also why two identical mono tracks will result in silence when one is phase reversed, and why Sharke is hearing a difference when he is summing the original bass track and the new one and hits the phase button on one of them. The number of channels in those tracks has nothing at all to do with it.
 
When you flip the phase of one track in a pair of tracks that are being summed, you will very likely hear a difference, whether stereo or mono. If phase didn't matter on mono tracks you could not null test with mono tracks (this is, of course, not the case).
 
Dean