Not familiar with that product, but sounds most definitely to contain Heterotrophic bacteria (these are the ones that break down/decompose organics/mulm into Ammonia).
Autotrophic bacteria are the Nitrifying bacteria. As Diana mentioned, they don't "eat" dead organisms, although the dead organisms being broken down by Heterotrophic bacteria into ammonia, could supply ammonia as the energy source for Autotrophic nitrifiers. However, in those bottled nitrifying bacteria products, to the best of my understanding, there is not ammonia bottled inside the products, the nitrfiers are simply in a extremely slowed down metabolic state (hibernation if you will).
The nitrifying bacteria you want are Nitrosomonas (ammonia-oxidizers) and Nitrospira (nitrite-oxidizers). They are found in Tetra SafeStart, Dr. Tim's One and Only, Microbe-lift Nite Out II
The bottled products usually last around a year if stored properly. Keeping it refrigerated (not frozen), slows down the metabolism even more, which keeps them alive longer.
For the original question of the thread, washing substrate with nitrifying bacteria is a waste. The substrate is just not a really good location for nitrifiers. Nitrifiers will want to colonize in the best locations, that being where dissolved oxygen levels and flow are most prominent which is usually the filter.
Nearly all of your nitrifying bacteria will be contained in your filter. Very little amount is on the substrate, walls, decor or in the water column. So don't worry about covering up the bacteria on the substrate. You can lose 50% of your nitrifiers and be fine. Autotrophic nitrifiers reproduce (double) in about 24 hours.
If you are still worried, add cleaned substrate to the tank, then just add the bottled nitrifiers into the tank water (or better yet, in the filter area), and just let the filter run so it can collect all the suspended nitrifiers.
Remember chlorine can kill bacteria, so always treat/dechlorinate the water before exposing the bacteria to it.