A custom tour through a company like Todo Turismo, Fremen, Expexsa or Hidalgo will cost a lot more, but you'll stay in a beautiful, heated, private hotel and have nice meals, better guides and better condition vehicles. However, all those companies (except Fremen) can also offer the cheapy-do deal like everyone else, where they just act as 'bookers'. and coordinate an available driver and guide.
There's a heckuva difference. If you can round out around 3 (or 4) people, then the custom tour is not massively more expensive, and very highly recommended. Otherwise, it's pretty steep (although I still recommend it). You certainly won't freeze or go hungry, and breakdowns (if any) will be dealt with much faster. Plus the really good hotels (not Mallku Cueva or the cheap Salt hotels) are amazing, and an experience in themselves.
If you want to do the inexpensive route, definitely follow schmuck's advice above - I agree with it wholeheartedly too. If you want the super memorable experience and a speck of spoiling (and are willing to cough up some major coin), go with the custom tour, especially if your needs will vary from what others in the normal groups of 6 or 7 tourists might want (i.e., longer time exploring some places, needs to approach sites more closely or differently in the 4WD, etc.).
Sorry to chime in again, but I want to be sure you know that there's a big difference, and are totally comfortable with your choice. Either way, the Salar is the Salar no matter whom you travel with, but the comfort and flexibility and number of memories can go waaay up with a custom tour. And orchid's right - it's not that easy to put together, or find other people looking for the same.
