marle seems to take damage better than the other 2
That's because Marle has the Prisim Dress, the most powerful armor in the game.

I personally never liked Marle for healing, I found AoE heals to be far more valuable than a focused heal. With Ayla in the party you have a spot healing tech (give her a few magic tabs and the amount heals skyrockets as it is based on her extremely low Magic stat) to support your main healer (Frog or Robo), and a way higher damage output. Not to mention Charm, which as shown below is invaluable.

The Black Omen is what you would consider the last dungeon of the game. You can run through it up to 3 times (1000AD ,600AD & 12000BC), but if you finish it in an earlier time then it is destroyed in all later time periods. (So go 1000AD-> 600AD-> 12000BC) The random enemies will all re spawn every time you clear it, but the mid-bosses and some enemies are only encounter able once.

Pay particular attention to the sentry wall panel things. You can steal a speed tab from each one, but they don't re-spawn. In one go through the Omen you should have easily enough Speed Tabs to max out full party at 16 Speed. Also the two headed snake things have Megalixers you can steal, and the enemies that look like the boss from the mystic cave have Power Tabs (and are respawnable) All and all Ayla is a must have in your party for the Omen. As mentioned earlier you can also steal a Prisim Dress and Helm from the final form of Queen Zeal, and you can fight her once for every Omen clear.