Theoretical question and an actual situation:

Assume a text book case:
Tenant is collectible, moves out, leaves damaged property behind.
You have $500 deposit. All rent is paid, but you charged $100 in late fees that have not been paid. You also have $1000 in damage and could prove it and the judge would agree.
Your lease also clearly states that any unpaid late fees can be deducted from the deposit and it would hold up in court (or your state law allows it already).

if your court is generally fine with late fees, no issues.
But if late fees are generally thrown out despite what your lease says, you would simply deduct the $100 form the deposit, keep the remaining $400 for damage and sue for the remainder of the damage ($600).

How do you write your statements to the tenant regarding the security deposit deductions to clearly show that the late fees have been deducted, and not something else (damages).

Here is basically how I've done it so far (with more detail, of course):
Rent owed: $0
Fees owed: $100
Damages: $1000

Total owed: $1200

Deposit paid by tenant: $500

Due by tenant: $600 within 15 days

If you bring that to the hearing, you couldn't clearly define what the deposit has been kept for and it could become an argument.
Do you state it in a particular way so it is clear which portion is deducted and what you are still suing for.

Again, just a theoretical discussion, I was just thinking of it while writing a statement. I am not able to collect from most my tenants (incl. this one) anyway.