Well ... the easy and uncomfortable answer is buses. They are cheap but take forever.
This is what I would do, fly from La Paz to Sucre and then take this scenic but bizarre train from Sucre to Potosi. Check it out:
http://bolivia.for91days.com/2011/06/05/from-sucre-to-potosi-by-train/ about 3 years ago
Take a "bus cama" from La Paz. There are two types of these buses, one with four rows and one with only three rows of seats. If you can afford it, make sure to get the one with three rows. One of the "Copacabana" lines that leaves from the central terminal offers this service, it's one of the stands near the entrance on the lefthand side as you enter the terminal. This is only an overnight service. about 3 years ago