Need to make sure its an official government website. There are other sites offering the same service and normally at inflated prices. I have using the official Cambodian online e visa service for years and i have never encountered any problems.
Not sure about now but that was the rule prior to covid restrictions. You needed to apply from outside thailand. The school should provide you with all the required documents that you would take to a Thai consulate outside thailand such as Phnom Penh who have many agents to assist with your application, you pay a standard price that you would pay the Thai consulate with an add on for the agent. All this is above board, no under the table so stuff. If you want your application processed quickly you pay more. The consulate in phnom penh has a good website and you can check what docs are required for education visa. I have used the same agent for years - they are on the riverfront in phnom penh. If you would like to contact them let me know as i have on telegram app.
All ED visa extension expire after 90 days - you can leave the country during any of the 90 day extension periods but will need a re entry permit each time. You can extend an ED visa by 90 days for up to 1 yr - then you need to start the whole process again. If you are going to leave thailand during the 90 days it is also best to get an official letter from school basically saying that you are a bonafide student and the school have given permission for time off classes. I know this from experience of friends.