Could just have a 'best available' system. The game knows what levels runes are. It knows every rune in your chest, left in the rune temple, on heroes in formations and even the guys in the closet collecting dust but holding spares. It knows those runes belong to you. It knows how much experience each rune has. The data persists between logins. So, it's stored somewhere. Whether it's in a nice format or not, who knows.

Wanna make some cash? VIP3 or so, preset formations perk.

Rather than saying "this extremely specific rune I now have at this level with this exp goes on this guy when I do this", have it something like this:

Preset 1:

Small formation grid. Black spaces empty, white spaces have numbers 1-5. Arrange to suit your need.

Dropdown: Hero 1, Hero 2, Hero 3, Hero 4, or Hero 5

-> Dropdown: List of hero names. Pick the one that is associated with the digit on the location in the formation.

--> Rune 1: Dropdown -> Choose highest priority highest level (Example: Morale)(It already knows that a +110 Partisan is better than a +50 Righteousness)
--> Rune 2: Dropdown -> Choose second priority highest level
...
Continue for all rune slots, even the not yet unlocked ones so you don't have to do all kinds of silliness every time you hit a level ending in zero.

--> Weapon: Dropdown -> Choose from 1-5, 1 being highest priority for best weapon (and being smart enough to put staves on mages and swords on everyone else) (And make a bow, please)
--> Chestguard: Dropdown 1-5 (Add checks to make sure same priority number isn't picked twice)
--> Helmet: 1-5
...

Save Preset As: <Text box>
SAVE|CANCEL

Wanna make more cash? VIP5 or 6? Smart Formations. Based on what you're doing when sitting around idle collecting dust and xp, it puts you in the events with the proper formation, or, when you click the button yourself to do some certain thing, it immediately picks the formation preset you specify. If you get revenged, it knows to have you in Preset 5. If you get tagged in the arena, Preset 2. Whatever.