I think a stop loss should always be used so it’s really only trailing or fixed to choose between.
It’s kind of just a habit that I choose fixed to be honest so definitely feel free to try trailing also and see what gives you the best strategies. You could set two identical reactors running with only difference being one uses fixed and one uses trailing and compare that way to see what’s generally giving you the best looking strategies. Or just set fixed or trailing in the generator so it can choose between the two, both options are all good.
For the portfolios I would definitely recommend working with portfolios rather than individual EAs but I would also recommend not having overly large portfolios unless they are very uncorrelated (which is not easy for same symbol and timeframe).
I would stick to portfolios of about 30 personally, just a preference to limit too many positions being opened at the same time but this really isn’t a big deal unless doing scalping that requires super quick executions. Opening too many positions at once can cause several seconds delay on execution which you will be able to see in MT4.
It’s fine having lots of portfolios on different timeframes and symbols (say 10 portfolios of 30 EAs) as it’s unlikely that for different symbols and timeframes trades will open at the exact same time. But again it’s really not big deal just what I do.