"Indicator appear" should detect only times when certain buffer goes from 0 to positive/negative value or from EMPTY_VALUE to positive/negative value.
Otherwise you can limit trades by time. For example using "Once per bar". After this block everything can happen 1 time per bar, as it's name says.
108 and 117 are at the top.
At the same time... if you use different Group number, this is like having different EAs, so in this case you can control 2 strategies at the same time in the same EA. This is the idea of the Group number.
If you want it 1-3-9-27, then this is Martingale with factor x3.
You have Strategy 1 and Strategy 2. Now because of the settings in "No position is running", especially in 115 and 125, you got two positions at a time, one from Strategy 1 and right after that second one out of Strategy 2. This depends on the numbers of blocks 108 and 117, in the case 108 runs first so Strategy 1 runs first.
If you fix blocks 115 and 125, then Strategy 2 does not work at all, because now it mirrors Strategy 1 in the upper part (from the first condition to "No position is running").
So I don't know, it works in the way it is build, I don't see bugs or something.
With so many different Buy and Sell blocks, better use their Comment section, and you will see the problems easier, like in this picrute: http://prntscr.com/4dyfgc
This is the idea, but if you want to check if it's working correctly, place some Alert message block after that one
Use "Indicator tester" block to check if the indicator buffers can be used. If they can... use them. The "Condition" block is working fine.
Only pink blocks and the pink category in "Condition" needs "For each Trade". Break even point does not need it at all, as it has the loop closed inside.
No, this block runs because of the current market where the EA is placed, and for that single run it causes the next block connected to it to run as many times as many market there are defined. At any iteration it sets the default Market parameter to different market.
There is no system that listens to multiple markets at the same time and reacts on each one individually. Well, adding the same EA on multiple charts works that way 
I'm not sure about the meaning of the question, but to limit things in one bar - "Once per bar"
By the way some connection is missing between blocks 25 and 26
Previous bar is already finished, the value should be the same. The only thing is that there is no need to recalculate the same thing again and again... if you have backtest speed considerations...
"Once per bar" makes things faster in this case.
But before "modify stops" better use "For each Trade"
Now check this: https://fxdreema.com/demo/mt4-loop-how-it-works
In MT4 you can have 1, 2, 3.... 100 trades at the same time. So when you want to do something with one of them, you must point to the right one. That's why I always recommend to use "For each Trade" block before using any other pink block from the same category.
I prefer to tell you how to deal with indicators
You can check any indicator if it works at all... using "Indicator tester" block. Like here: https://fxdreema.com/demo/mt4-indicator-tester
There are few possible values
If you have the same value all the time, let's say the EMPTY_VALUE, then the indicator does not use it's buffer properly or you have to change something - try with Candle ID. Often indicators work on the previous candles, not on the current one.
Try with some block from Indicators category. For example "Indicator appear". This should detect the moment when the indicator appear on the chart... in case the indicator shows some arrow. If it is MA type (always appeared), this block does not work for you.
Use "Draw arrow" to check if some block passes. You will see arrows in the places where the block passes.
Hold the mouse over any block and ? will appear - click on it. Or right-click on a block and go to "Information". Or click on "Help" on the main site, where you will see very simple list of the main 3 outputs, and what each one means: https://fxdreema.com/documentation/
Condition = If. If something... This is a check, not an action. Please, look at the examples!
If we are talking for CONQUERER 3, there is nothing in there for SL, trades are created without SL/TP, and there is nothing else to modify it later.
The same with CONQUERER... and I think something is missing in the Buy now block.
There is something wrong with these two. There are two block groups that finish with "Condition"... why... no reason here. I told you that there are some rules.
Look here to see which block runs first: https://fxdreema.com/demo/blocks-execution-order
And here to see the basic events: https://fxdreema.com/demo/mt4-events
And here for more basic examples: https://fxdreema.com/examples
The problem with OR blocks is that they are not supposed to be used that way. There are some rules. Check this one: https://fxdreema.com/demo/blocks-execution-order
What's wrong with the trailing stop block, it can work with virtual stops as well
On the Buy side, when the price is going up block 402 passes often (better use > in it), but then when the price starts to fall down it does not pass. You want to modify "atr_stop_buy_grid" when needed, but check it all the time in order to close trades.
The answer: Break the connection between 403 and 404
I think Scripts work. No one complained lately, but not many use it, so...
You can try it anyway, for small experiments like this it's totally free.
Yes, fxDreema reads the .mq4 file but only that part where input parameters are defined. It does not include the indicator itself in the final EA, it does work with it, only gets some information once and that's all. Optionally you can manually input that information, but it's faster to upload the file so fxDreema can read what is needed - this is the only idea
In the past it was possible to read this data from .ex4 files, but now everything is encrypted and even this data is not cisible from there. But .dll files have nothing to do with input parameters, so... not needed.
http://prntscr.com/4c6te4
This is the same as just checking if one of the values is > than the other. You don't need this Formula.
Also somewhere I saw "OR" blocks... in general these are also not needed. Especially in serial connection like this: http://prntscr.com/4c6u66
That option "% of Equity => Lots" is some simple calculation, which means that if you have 1000 dollars, 100% will equal to 0.01 lots, (when 1 lot is 100000). In this case 2% is something very very small and the minimum will be always taken.
Indicators produce numeric values for the EA, so the EA have to check those values in some way or another, and make decisions what to do with them. Because custom indicators are so different, first you need to know what values your custom indicator is giving to the EA and then use them properly. Use "Indicator tester" block to check indicator buffers if you don't know what they return to the EA. Then... depends on what needs to be done... Condition block(s) or some block from "Indicators" section.
What means breakeven for.... I guess running orders. Something like this maybe: https://fxdreema.com/shared/5MJFmst2d
What, if you have buy trade to place it's stop at the lowest price since the trade was created? I think I'm missing something, because doing this is basically closing the trade right from the beginning or pushing SL further and further so it can't be reached (at least until the EA is removed).
If you want to place SL to the lowest value back in the history (for some time), then something like this: http://prntscr.com/4c34n8