The total number of native assets in input and output should be same in Multichain. Hence if you happen to manually select input and output in such a manner that the the total number of assets in input and output are not same, the signed transaction will not be getting accepted with an error 'Input and Output Balance Mismatch'. The transaction shall fail. I think if you need to implement fee for transaction, apart from spending assets in input, you may put native currency as well in input which would be used as fees if configured.