For the Subnet-EVM, transactions are paid for by the native token of the platform. You can define initial balances on your chain by setting its genesis to give whatever addresses you want an initial starting balance.
Only 1 token can be used for the network fee, and this cannot be split between multiple tokens.
To learn more about Subnets please read the following article.
For any additional questions, please visit our knowledge base or contact a support team member via the chat button at support.avax.network.