Secret Coins are found through all of the Main and Crew episodes. You will find that each Main episode has three (two being special conditions, and the third being S rank) while the Crew episodes only provide one (S rank). The earliest you can get this is with the very first stage, the introduction to the game itself. For this stage, I'll reveal the conditions you need for the Secret Coins.
*** Spoiler - click to reveal ***Secret Coin #1: Follow through Nami's plan to completion.
Through the stage, you'll see text prompts from the other characters. Nami will concoct a plan to get you through to Eneru, and needs your help to see it completed. As soon as you end up getting a Mission Complete notification, you will see "Treasure spotted!" message as well as a notification on the mini-map. This is where a gaudy treasure chest is located.
Secret Coin #2: Defeat Smoker with all of your allies.
You must first make Smoker appear to get this objective started, and that requires a thousand kills before moving to face Eneru. Once you do this, you will see Smoker spawn on the left side of the map. Make sure that none of your commanding officers flee before you slap Smoker around and send him running. I do not know if this merely counts your named officers (like Nami or the other Straw Hats) but if you fight alongside your friends and take care of the enemy officers around them, they should have little to worry about.
Secret Coin #3: S Rank.
This may be a bit more difficult, especially if you're just starting out on the game. S ranks are calculated through the three sub stats that you see at the end of every battle: kills, damage received, and time. Kills will usually require 1100 or more to get an S rank, even on smaller stages. Damage received can be a bit tricky so aim for keeping officers away and using your Musou or Style action to deal plenty of damage. Style Action can also help in getting kills faster, though the timer can be brief early on and take forever to build back up (unless you find some Mizu-Mizu meat, shishkebabs, or rice meals). Generally, don't spend too long on a stage, though I personally don't know the exact time to measure for each. Keep the battle flowing and kill the enemies while you conquer the mini-objectives, or return when you're stronger so they pose less of a threat.