Provent-A-Mite is good when you follow the instructions it comes with. A thorough disinfecting of the enclosure & all cage furniture is beneficial as well, as is a thorough vacuuming of the room, and disposal of any loose substrate where mites could hide. Getting rid of mites on the snake itself is the easy part. Ridding your snake room of them is where it can become tricky. Fortunately there's a lot of good info on this forum about mite eradication.
First off though, have you *positively* identified the flecks in your snake's water bowl as mites? As they could be bark from a log hide, bits of substrate, etc. It's good to be tuned in to your snake's behavior & his environment, but also look at other factors - i.e. could he be soaking in the water because his other hide is too warm/cool? Or maybe, the snake is just soaking. It's OK for them to soak, you just want to rule out all other factors (i.e. hides, heat, mites) in the event that it becomes excessive. For example, a snake soaking for a few hours here or there usually isn't a worry. If you observe repeat visits to the water bowl, then it's time to really key in on the cause.
Again, it's great that you're being so observant, especially as a new keeper...that's a really good habit to get into!Just remember to check up on all the simple causes of a specific behavior before you just focus on one big one. i.e. when you hear hoofbeats, rule out horses before you go looking for zebras.
Good luck!
K~