To control them independently the Canon speedlite system has a concept called "groups". All flashes in the same "group" will get the same settings... but if in different groups they can have different settings.
E.g. you can put one flash in "Group A" and the other in "Group B".
By default you might see the word "ALL" on your LCD which means the settings are being applied to ALL speedlites regardless of group. But if you can switch groups and change the settings or you can use the "ratio" option.
If you use the "ratio" feature then you can, for example, set a 2:1 ratio which means one light should provide twice as much light as the other.
Or you can ignore the ratio and just go into the groups separately... e.g. set the flash exposure compensation on one group to fire at half-power and leave the other group alone -- which would be roughly the same thing as using the ratio feature.
What I would NOT do is attempt to have one flash in E-TTL and the other in Manual mode (I've never tried to do that and I"m not even sure it's possible.) Normally ALL flashes should be in the same mode. If anything is manual then they should all be manual. If one is E-TTL then they should all be using E-TTL.
Your answer is very clear but the thing is that in one of Bruce Dorn YouTube tutorials about those speedlight he did set the flashes in differant mode.
When I tried it, it did give me this possibility but when i tried to take a pic the speedlighs radio transmitter change the setting.
So that's why I was confused.