I'm not sure what you are trying to ask... or explain. But judging from your topic title, I assume that you are either asking what the best way to clean gravel is... or telling us what the best way to clean gravel is.
Cleaning gravel is essentially the same process, whether you use something like a python, or just a standard gravel vac and bucket. The only difference between these two processes is how one draws water out of the tank and thus producing a vacuum in which you can use to clean your gravel.
Most (if not all) people generally do water changes as they clean (vacuum) their gravel, minus some circumstances. After establishing a vacuum on your gravel vac, just stick the vac into your substrate (as close to the bottom of the tank as possible) and let the water vacuum do the work for you. What I generally do is leave the tube in the same area until the water is generally clear, then I move onto another section of the tank, paying closer attention to areas of the tank that seem to collect more debri (after working with your tank for a little bit, you'll get to know where debri tends to collect more often). This may be time consuming, and may take a lot of water out of your tank... but if you stock moderately, feed lightly, and do this often, you should be in good shape.
I'm glad you brought up the subject of bacteria. Quite a few beginners are somehow lead to think that regular gravel vacs will damage their bacterial colonies. In fact, regualr gravel vacs will do virutally nothing in terms of damanging the bacterial colonies in your tank. With the proper filtration, most of your bacterial colonies should inhabit your filters... (unless your running a gravel filter of some sort, in which most ofy our bacteria will be in the gravel)
-Richer
