Via the Tools-->Options, ATI Tab you can set the following stop order handling options:

If you have "Submit market order on TS fill" enabled via Order Handling Options, the following Stop Order Handling is ignored.
Submit "as-is"
Submits the stop order as specified.
Convert to stop limit
Will convert a stop order to a stop limit order. The limit price is calculated based on the user defined "Limit price offset as ticks" value.
Convert to simulated stop market
Submits a simulated stop market order which is a local PC held order that submits a market order once the stop price is hit.
Submit market order if stop order was rejected
Submits a market order in the event that a stop order is rejected for any reason.
Behavior as follows:
DISCLAIMER: If this option is enabled, it is your responsibility to ensure that your TS EL code is sending valid stop prices to NinjaTrader otherwise you risk getting filled when you may not want to.