I'm manually moving the transients of the bass line, to line up closer to the drums. I will have to test and see which settings respond best for bass, keys etc. It will be a great tool if I can figure it out. I think I was trying to do too much. I'm not going for perfect here...I just want it a bit closer, and I want to learn how to use another tool.

WRT the warble you mention in post #3, AudioSnap uses two different rendering techniques.
 
If you are moving the transients around and just going back to listen ... what you are hearing is an on the fly rendering.  It gives you a good indication of whether you've moved your peak to the correct location but you will definitely hear artifacts like warble, as it is a quick and dirty, low processor load render.

When you render either by bouncing to a new track (or by exporting your track), a high resolution and time consuming render is performed.  So, if you are just evaluating on the fly you could probably just ignore the warble because it will probably not be there after you bounce to track (or export).
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Alternatively if you are just manually moving a couple of peaks (and if it was me), make sure ALL of the transient makers are off before you start and just highlight and move the ones of interest.  This allows Audio Snap to decide how to move all of the surrounding information in a musical way.  Then you can go in and add more transient markers in an intelligent way to get the desired effect.

If you turn on Audio Snap and there are a whole bunch of transient marker already assigned and you move one marker within the whole mess of markers Audio Snap will do exactly what you tell it to do and may squeeze notes together in an un-musical way.
 
To get the best result (and it takes a fair amount of practice) is to make sure you know the where and why of each transient marker WRT its position before moving.   
 
 

i don't use it.
 
i don't even know what it is!~

I've used it to loosely quantize multi tracked drums that were a basket case in some areas and it saved the day. It works well for rogue bass notes etc. The main use for me is for creating tempo maps for imported audio. If I have a click track I use that if not I use the kick track. I usually track to an Alesis HD24 and import the tracks into Sonar.
 
Rocky

I have tried all of the render settings, but I always bounce to clips...maybe I should try bouncing to a track?

The following is just observation / speculation / guessing on my part:
 
Whenever I set-up to use Audio Snap I resave my project (working mix) with a different name and then depending on what I am doing I either bounce to track and copy and paste that rendered track back into my working mix or export and then import the track back into my working mix.  Audio Snap, properly used is a very powerful tool but it gives me anxiety.
 
I wouldn't bounce to clip, I would bounce to track so I could listen to the render and then make changes and re-render if necessary.
 
If by bouncing to clip it is truly rendering and you are still getting artifacts, then my guess is that something else is going on ... it is not the bounce itself but how things are moved around.
 
Most of my experience is on drum tracks so here is an example from my experience that is probably not relevant but I will throw it out there.  Say for example I want to quantize a track and inadvertently ascribe transient markers to a series of 16th notes but set the resolution to 8th notes.  When I render, Audio Snap will force the 16th notes to line up where the 8th notes should happen and squish the notes together in an unmusical way.
 
The point is, the surrounding notes will influence the quality of your result and can result in weird sounding effects.
 
Other things that can cause weird effects are stretching a note too far or multiple renderings (that is why I bounce to track ... each evaluation is an independent rendering and when I am done the resulting track has only been rendered one time with Audio Snap).