In general, if a repair costs more than $100 and the damage was caused by a student accident (cracked screen for example) then yes, you would charge the $100 deductible. If the repair costs less than $100 (replacing a missing key perhaps, or replacing a power adapter) we only charge the cost of the repair.
If you suspect the problem with a laptop might be covered under warranty (for example, the unit will not power up and no physical damage is evident) then open a work order for us and we will let you know if covered or not. Apple will either process the repair very quickly, or will send us an explanation of why they will not cover it. An example of that would be where a student spilled water over the unit, causing hidden damage. In that case, you would then charge the $100 deductible.
In cases where a student maliciously or intentionally damages a computer, the full price of the repair is charged to the student. Always get agreement on this with the local Principal before charging.
I put together some notes regarding cost of common repairs at the end of the year last year, as we were collecting laptops from all students. Look at page 3 of this document and see if it helps you to make sense of this all: