Many people end up making the alignment process far more difficult than it needs to be because they don't understand the fundamental difference between "near field" and "far field" alignment. At the expense of sounding didactic, allow me to explain.
Near field alignment is how close to perfectly overlapping the beams are AT THE DICRHO FACE. This is the most crucial part of any alignment, and it's the part that most people get wrong. If you find that your alignment looks great at 20 feet, but horrible at 40, then the problem is your near field alignment.
Near field is always the first thing you adjust. Unfortunately, most projector designs don't leave a lot of adjustment for the near field. Usually you end up having to shim the lasers on the baseplate, or moving the dichro mount forward or backward along the beam path (or both). Because it's such a pain in the ass to get it right, many people skimp on the near field adjustment. And that causes problems later on.
There are some advanced projector designs that add an extra bounce mirror prior to the mixing dichros, and these designs give you an extra adjustable mount that you can use to tweak the near field alignment. They are very easy to align, but they cost more because of the extra components and the larger baseplate, plus there are additional power losses from the extra bounce. (Here's an example of one such layout: )
http://photonlexicon.com/gallery/d/10380-1/layout.gif
Regardless of how the projector is laid out on the baseplate, the near field alignment absolutely must be dead-on. That is, the two beams must overlap perfectly at the face of the dichro. You can test this with a decent set of neutral-density goggles, but it's tricky, as you need to be fairly close to see the dots overlap. Alternately, you can display a white pattern and look at how the lines appear when they are projected VERY close to the aperture (just a few feet away). This is less accurate, but in cases where you have easy adjustment of both near and far field alignment, it can sometimes be quicker to align the projector using this method vs inspecting the overlap at the dichros.
Once your near field alignment is perfect, THEN you adjust the screws on the dichro mount to bring the beams into alignment in the far field. In this case, far field is taken to be some significant distance away from the projector. As a general rule, you want as long of a throw as possible when adjusting your alignment. I do it in my back yard at night, and I fire across the yard on a diagonal to get 100 feet or more of throw. For sure you need to be at least 25 feet away, and even at that distance you may still be slightly off and not know it.
The key to remember is that the adjustments on the dichro mount are only for the far field alignment. They will not do you any good for adjusting the near field. To get your near field right, you have to "steer" the beams onto the dichro face so they overlap. Then you can adjust the angle of the dichro face (using the adjustment screws on the mount) to bring the far field into alignment.
If you don't have the advantage of the extra bounce (as in the picture above), then you need to physically move the lasers around on the optical plate to adjust your near field alignment. Some people have even mounted each laser on a "floating table" (basically a plate suspended by all-thread at the corners) so they can adjust the height of the laser by turning the nuts that hold the floating table to the all-thread rods. But that only helps with height adjustment - you still need a little bit of play in the horizontal plane as well. (This is where a movable "foot" on the dichro mounting bracket can come in handy.)
Finally, you don't need fog to adjust your alignment. The best way is to simply display a white test pattern (the LaserMedia test pattern works really well) and then look at the horizontal and vertical lines to ensure that they appear white, and that they don't have any fringing. When I adjust my alignment, I have half the patter displaying on a surface that is very close to the projector (less than 5 ft), while the other half is landing on the fence at the corner of the back yard. When they are both perfect, your alignment is also perfect. (But again, I use the double-bounce method above, so my alignment is a snap.)
Adam