Abilities: First of all, you should do your best to keep their Abilities at the maximum level at all times. That's expensive and it will take a while, so start with your best/most favorite hero and work your way down to the least favorite. I recommend upgrading them all to at least half their maximum level first, then work up with the upgrades until you max them out. All players get the same 5 starting heroes no matter what, and I would recommend leaving the Archer (Demetra) behind as she is the weakest hero in the squad. I recommend focusing on maxing out the rare hero first, the healer and the fighter in that order. As you play more, you will unlock new and better heroes which will replace the worst in your team. This is why it's better to try and work on them one at a time, from the best to the worst - if you unlock a better hero in the mean time, you wouldn't have wasted precious resources on upgrades.

Runes: You collect Runes randomly as you win various battles and they work in a similar way to abilities: they grant all sorts of bonuses and can be upgraded. I also recommend upgrading them a lot, especially since they use a different kind of resource (Gold). The good thing about runes is that you can equip and unequip them as you see fit, so you can't go wrong with them in the long run: there's a ton of rune slots available so all upgrades are welcome.

Rank: The rank of your heroes is extremely important: the higher their rank, the better their stats. The good thing about the items required for ranking up your characters is that you can simply tap them in the menu and then hit the "get" button: the game will automatically take you to a mission that can drop them for you. Either go for the raid tokens or go through the battles manually, and you will eventually get them all.