Using stops is very simple, set LongInitialStop=10,ShortInitialStop=10. The real stops of individual orders will all be set at the same place, which is the price of the last order + Pips+InitialStop. This way, if one order is stopped out, all will eventually be stopped out and closing the trade is what Bipolar does.
Using stops has the advantage that your risk is clearly defined and you can start improving the expected value of a trade. This is impossible if you have to judge the risk of blowing the account and the probability of this event. I prefer having a consistent win/loss rate that allows you to do proper money management and risk of ruin calculations etc.

Yes, I used only the above mentioned signal, you have to experiment a bit with timeframe and lag, but experiments with other signals didn't really improve the result. Only the TrendFilter of Bipolar is useful. However, if there is a consistent expected value of a trade, you want to have as many trades as possible and to compound the gains. That's the way to optimal profit. The TrendFilter improved the results but also considerably cut down the number of trades. So the total result is less profit, but maybe with less risk (drawdown).

I think using ATR will help, whether it is used as a filter or to vary the pips and t/p and s/l values. You only have to properly scale everything, including lot size, in order to still have the same max risk.