All of your Ships do the same as you tell them all at once, so when you give the attack command, it´s not only your flagship that does fire, its all of your ships at the same time.
Also, when you loose just because one of your ships was destroyed, it´s most probably because it was you flagship, thats the first one on your lower topscreen where you see the HP of your ships.
Best way to prevent that is to change the formation of your fleet. To do so, go on a planet of your choise to the "CTA" screen, there you select "Edit Fleet" which gives you a screen where you can edit the formation your ships are flying in. there you put one ship in the right row, one in the middle one and your ship marked as 1 in the left one marked as B I think.
That done your flag ship is guarded by your other ships when attacked by the enemy which means it´s far more hard to hit it as long as your other ships aren´t destroyed first.
Also, when you loose just because one of your ships was destroyed, it´s most probably because it was you flagship, thats the first one on your lower topscreen where you see the HP of your ships.
Best way to prevent that is to change the formation of your fleet. To do so, go on a planet of your choise to the "CTA" screen, there you select "Edit Fleet" which gives you a screen where you can edit the formation your ships are flying in. there you put one ship in the right row, one in the middle one and your ship marked as 1 in the left one marked as B I think.
That done your flag ship is guarded by your other ships when attacked by the enemy which means it´s far more hard to hit it as long as your other ships aren´t destroyed first.