How can I make sauerkraut to best preserve the probiotic elements?

The ingredients of sauerkraut are very basic--its basically just cabbage and salt (the water is drawn out of the cabbage). Given this, you will produce the most nutritious kraut using high-quality cabbage and salt with natural minerals. A high quality sea salt will contain additional minerals that processed kosher and table salts lack (also, it is typically advised not to use salt with iodine--as it apparently prevents the growth of the desired bacteria). Additional ingredients such as spices will add their relative nutritional value to the mix.

Obviously this doesn't necessary maximize or preserve any "probiotic" aspect in particular, but as commenters have mentioned these claims are dubious as best.

Also, by the way, you only need to add water if the cabbage fails to produce enough brine to cover it after being salted. If you do add water you'll want to add additional salt so as to preserve the salinity--typically I've used 1Tbsp of salt per quart of water.

I usually leave fermenting vegetables out for about a week. Some variables in the final product are crunchiness and sourness, which I believe depend on time, temperature and the amount of salt used. You should taste your kraut a few times over the first few days to see how you like it, and when you think it's done then cover and put in the fridge to stop the fermentation.

By the way, you want your vegetables completely submerged to get the anaerobic effect, and you may see some foamy scum on the water surface which is harmless. You can skim and throw it away if you like, or just stir it down into the mix.

The bacteria that cause spoilage can tolerate salt concentrations up to 7%, while the desired lactobacillus strains prefer a 2 to 3% range. Therefore the correct amount should be used. Above 7% the food would simply be preserved, without pickling. When it comes to pickling the purpose of the salt is to draw carbohydrates from the vegetables in order to provide a food source for the desired bacteria. The metabolic process of the bacteria then creates an acidic environment.

Temperature of at least 18 degrees Celsius is required for fermentation which should occur prior to transfer to cold storage (fridge or cellar temperatures).

Keep the vegetables submerged in the brine. This creates an oxygen free environment that encourages probiotic growth and discourages spoilage by mold, bacteria, yeasts and fungus. It also preserves vitamin c and other antioxidants.

Minerals besides Sodium Chloride (pure salt) can have detrimental effects. Iodine can cause discolored brine. Magnesium can impart a bitter taste. Iron can cause discoloration. Not serious problems, but avoid salt with lime as it is alkaline and can prevent the correct acidic environment.