Now that you have somewhat an idea of what Paint effects are and what they can do to you, I will proceed to tell you how to work with them, or at least how I have found useful to work with them.
Since we do not have an Alpha channel I plan accordingly and render all of them at once (in the images I have showed you the red nebulae, the stars, the sun and the glow line are each different paint effects strokes).
However, when we absolutely need an alpha for whatever reasons, there are work arounds one can employ which basically create an alpha channel for you in much better state than the one that comes default from Maya. There are several ways to do this, I will now outline a couple that I find to work the best:
keying out the black is an obvious choice, and although at first it sounds hopeful it is not that easy, or rather, the results are not that great, especially with glowing things, which is about all of paint effects.
here is a paint effects image in the raw, as it came of the renderer and with its alpha ignored
Now here is one with a color key applied
although at first it might seem promising, look at a close up of what the key looks like
after some work with the key
and a close up
now this looks much better, until you go back to the original one and realize how much detail you've lost
another method is the shift channels method, where you take another channel of the image, say the red channel or the luminance depending on what would be best for that particular image and make it the alpha. the downside of this method is that you can adjust it very little, but for particular images, say if we had only stars which are mostly luminance with almost no hue in them, it could work very well.
same image with shift channels applied
The only way to control this method is by using individual controls on the levels and adjusting, of all things, the alpha on it, which is basically its luminance.
In my opinion the second method gives somewhat better results although it really depends on the image.