While transferring ada to atomic wallet, I also sent a secondary coin, incompatible with atomic wallet.
What should I do?
Wait for the smart contract (I think)
I would also recommend waiting, though instead for Atomic Wallet to support native Cardano tokens besides ADA (“secondary coins”) because they have not been friendly with providing this kind of feature or support, and you would need that support to get the tokens now. They use a proprietary method of key generation, meaning that only someone knowing Atomic Wallet internals could help you get the private key needed to transfer your tokens out of the Cardano address (UTxO) where they are located now:
If you find someone in Atomic who can help generate the private key (and I have heard getting this kind of help is difficult), you could do the transfer out manually with cardano-cli. Warning: working with raw keys is a high security process that can lead to losing funds if you store that key even for a second on any machine connected to the Internet.
For all these reasons I’d suggest to wait until Atomic Wallet announces & supports “native tokens” or “native assets” as they may call them. Waiting for smart contracts won’t help you with the fundamental issues of 1) not knowing the private key for your wallet addresses and 2) not being able to refer to the tokens stored at those addresses. The tokens should be safe at those addresses in the meantime.