1. Both these are possible because the first sentence uses a present continuous for an arranged future. (e.g. I am seeing the dentist on Friday.), while the second is a simple future tense. There is also a third option 'You will be making up for the class on Monday 13th'. This says that at this time in the future the students will be performing this action.
2. Temporal indications such as 'tomorrow' can come at the beginning or end of a sentence or major clause. Usually we put the more important aspect of the indicator first. So if the important thing is the 4 o'clock part you would say '4 o'clock tomorrow'. However if the important aspect is that it will be the next day, then use 'tomorrow at 4 o'clock'.