OK...newer to the BSA side here...

One organization with multiple accounts, all with the same TIN...

Acct 123: withdrawal of $10500
Acct 456: deposit on $180

I know that I do not net these amounts, but do I list both transactions on the CTR, or list just the withdrawal?

You would only list the reportable transaction... the 1 over 10,000.

So to help me understand better, why not both transactions?

There is room and blanks for both amounts and types of transactions, why not list all cash going back and forth over the counter?

If the cash deposit was in excess of $10,000 you would list both. However, since it is beneath the reporting requirement it does not get listed.

If cash received by the bank in one or more transactions by or on behalf of the same person exceeds $10,000, the cash received transactions are reported. If cash received does not exceed $10,000, do not report cash received transactions.

If cash paid out by the bank in one or more transactions by or on behalf of the same person exceeds $10,000, the cash paid out transactions are reported. If cash paid out does not exceed $10,000, do not report cash paid out transactions.

If reporting both cash received and cash paid out transactions by or on behalf of the same person, report both on one form.

Remember that currency exchanges are counted as both cash received and cash paid out.