These are your primary units. Usually you're going to want epic silver or primarily Gold heroes here. Build these heroes with the strongest gears, beasts, and skills you have. Typically you'll want these heroes to have high leadership stats and gears that boost the effect and launch rate of their special skills. That should be your first and foremost focus. Second you should work on either increasing defense or offensive capabilities of the hero. This can be done one of two ways, increasing def/atk metrics, or increasing damage/damage reduction. The most effective will be damage or damage reduction, but those metrics are harder to find and also don't top out as high as necessary. There are beasts that can further reduce damage or increase damage dealt for your units. Skills that you definitely want to try and find: Archer/Infantry/Cavalry Commander, Yin-Yang, Illusory Force/Fortitude/Rattan Aegis, Linebreaker/Kamikaze/Horse Bane. All these skills are fairly common to find, and they also cannot be affected by anti-skills like swelling resistance (which reduces the effect of blood battle, melee master, cavalry master, archer master). Other crucial skills to be on the look out for in the school are Heaven's Blessing and Swelling Resistance. These two skills negate the effect of other common skills like cavalry guardian, archer guardian and infantry guardian and adamanta (Heaven's Blessing). The next thing that would be imperative to get is specialty and proficiency scrolls. This will further increase your launch rates and effect of your skills. Again, that should truly be one of the first priorities, but unfortunately unless provided by an event, the specialty and proficiency scrolls are rare and only appear in the highest levels of the school.
Be advised that using a Chief Strategist will cost you double food every round with very few heroes being an exception (Madame Mi, Madame Gan, and other support heroes don't require food to do their support skill). That being said, why would someone want to use a strategist? Well for one, you'll be able to deal a lot more damage per round. So effectively if your kingdom has the same amount of troops as the other kingdom but your kingdom is using strategists, you should in theory be able to easily wipe the other army. One additional benefit is increased attack metrics. Also if you're running a full team (with deputy commander), then you get an additional 50% defense bonus. So who should be a strastegist? The support girls make a good choice, but only if you're using effect gears so that their effects don't end at the end of the current round the skill is cast in. Strategists typically move last because their stats are reduced to 20% (including leadership, which determines order of hero move). While using the support girls you'll have to worry less about food because when they cast it doesnt take food. Other good heroes for strategists are stunner heroes such as Hua_Xiong or Wen Yang. Other choices that are perfect for strategists are heroes with black arts like Zuo Ci and heroes with flaming arrows like Taishi Ci. This will cause burn damage the next time the hero targetted moves. As far as equipping gears and beasts go for strategists, only focus on offense. Leave defense for the chiefs and deputies.
Deputy Commanders are defensive only units. The only types of bonuses added to the troop unit are defensive ones, and the only skills that proc are counterattack or defensive skills such as Pitfalls. You will probably want to build these units with Leadership as their primary attribute and intellect as the secondary attribute.
Gears: Equip them with gears that will increase defense measures or reduce damage taken. Do the same for beasts, although it is still unclear as to whether beasts do work on deputies and strategists.