If transactions require a fee in your blockchain, then you need to take account of this when generating those transactions. In the case of an atomic exchange, this means that one or both of the participants must cover the fee. They can achieve this by adding in some quantity of the native currency when calling preparelockunspentfrom, e.g.:
preparelockunspentfrom 1... '{"JPY":10500, "":0.001}'
In the example above the empty asset name ("") is used to denote a quantity of the native currency.
As to the exact amount of native currency to add to cover the fee, you'll have to calculate this based on minimum-relay-fee and the expected size of the final transaction, which you can learn from previous examples.