Why don't we just have it so we can attatch a champion (or your sovereign) to a similarly armed squad (archers to archers, etc). The way I see it, champions are (fundamentally) just substantially more powerful regular units. Being able to designate them as squad leaders would be the simplest way to greatly extend their usefulness.
I personally think that warfare Champions should have limitied usability in middle/late game by themselves compared to magic Champions. Unless they have been totally buffed up by the Sovereign with uber artifacts, mutations, blessings and who knows what more, the warfare oriented champions shouldn't stand a chance against (great) groups of (trained) soldiers. With class/skill-trees (plus some kind of unit attachment), warfare champions can still be useful (even if unbuffed) with skills that allow them to increase combat efficency of their units, recovering broken (morale) units...
Magic champions only need proper magic system/spells to be kept useful during the whole game... and be careful of stones, javelins, arrows, flying cows, spells, dragon's breath, mountains summoned over them... Which doesn't mean that they cannot also have skills that can benefit mundane units.