A Gallic army can have up to eight commanders in all. I would recommend fielding as many as you possibly can, ideally one per non-skirmish unit.
Did you remember to give your Gallic units the Warband special rule, which adds their Combat depth and formation bonuses to their Cohesion value, up to a maximum bonus of +2, for all Cohesion tests?
There is no need for each opposing unit to be of equal point value. The Gauls should have more units that the Romans – that is one of the chief advantages of fielding less expensive units! I also would advise not allowing the tough Roman legionary units to 'double up' on your warbands. If you want to add bases to make your warbands more durable, I would suggest adding a third rank of bases, rather than making the formations wider, and thus more vulnerable.
Throwing spears and heavy throwing spears are not used in the Shooting phase. They are used for the first round of Combat only.
Skirmishers may move through/interpenetrate other friendly units, and other friendly units may move – but not charge – through skirmishers. Using the Escorts special rule, a formed unit may charge through accompanying escorts that are in skirmish order. No other types of unit interpenetration are allowed.
Small units of troops armed with ranged weapons should be used in their historical roles to skirmish, screen, protect flanks, and harass enemy troops. On the other hand, larger units of massed missile troops can have correspondingly greater effects and be much more decisive, which seems quite historical to me.