Mother Trinity tips to save health and items.
1st stage: 3 pod things. Attack the one with the sword and the one that look like its not doing anything (but it's making the electric orbs appear). Stand on the whiter tiles because the orbs can't touch you. Try not to kill the pod that is shooting electric beams at you. That one is the weakest and once you kill the two pods, the one remaining will be strengthen.
2nd stage: Mother Trinity and the remaining pod. I didn't kill the remaining pod because it didn't deal that much damage to me, but you can if you want. Head for one of the corners near Mother and stand at the tip. This way, she can't reach you with any of her attacks except one, where red circles will surround you and lighting stuff fall on you. Dodge this move by running around (near your corner) and return to the corner when she's done attacking. It's easier to snipe her if you are in the corner. Keep attacking until she dies. Don't worry about reviving/healing your team because they don't really help and will be revived for next battle anyway.
(Dark Shadow thing)
1st stage: Attack from behind (try to) and preferably at a distance so you don't get hit by the orbs. When he dips his face into the ground, start running because it might mean that the spike things will come out of the ground. Running can avoid it. Also, don't stand directly behind or next to it because he has this other move that has dark beams that go from his direct east to west and north to south. So try standing diagonally. He also has this beam move that depletes your health to 1 hp but it only affects those that are within his front range (thats why you need to stand behind him).
2nd stage. He has basically the same moves except he can swim around. Just stay out of his way. What worked for me was to stand really near to him (to his left or right when he's up against the wall) so that way, his frontal attacks don't reach and I can easily dogde his swimming moves because he can't swim into the wall. He will use the same attacks so make sure you run when the spikey thingies come out of the ground.
Good luck!