We have a customer who deposited $9,000 in US currency and $10,000 in EUROS which converted to $12,487.00 in US. In part II box 26 of the CTR we will enter the total amount of currency US and foreign (converted) currency $21,487.00, so in box 26a are we to enter the actual amount of foreign currency which is $10,000 or the convered amount of $12,487.00?

Looks like you'd use US dollars, this is taken right from the CTR instructions:

If foreign currency is exchanged, use the U.S. dollar equivalent on the day of the transaction (See “Foreign exchange rates”),and complete item 26a or 27a, whichever is appropriate.

The instructions for items 26a and 27a require that you insert the UNCONVERTED amount of foreign currency, so you would put 10000 (note, no currency symbol, and certainly not a $) in item 26a and "EE" in item 29 to indicate which currency is reported.

You are correct to put the total US equivalent amount (21487) without a decimal point or cents in item 26.

Makes perfect sense, thank you