[Velusion]

Company vs Squad?
I much prefer bigger companies because they are harder to break via morale.

Spread Amongst Commanders?
Again - the bigger the company the stronger via morale they are. Splitting up decoys (for archers) is a notable exception. Also some troops you want to keep separate (e.g. those that radiate heat/cold.
My understanding (and I could be wrong) is that when a commander routes it simply lowers the morale of your troops, but does not make them automatically flee. Also I get the impression that if all the commanders on your side flees your troops will break very easily.
I typically never let my normal commanders enter the fray (though there are always exceptions).

Using Cannon Fodder
Cannon fodder should be used to
a. Decoy archers... you don't need a lot of troops to do this.
b. Absorb spells like Mind Burn / Soul Slay. Your goal is to either wear out the mages or at least absorb some of the spells.
c. Take hits as a meat shield so your casters can do real damage.

I would recommend putting your fodder up front on one side of the battle field set to "attack closest" and put your thugs/good troops slightly behind them on the other side and "hold and attack rear".

Using Trample Troops
Totally depends on your opponents setup and what else you have in your army. Default I'll usually put the tramples close to the front with a very light screen in front of them to absorb the inital hits.

Other Tips
Big army vs. army battles are very difficult to pull off. Experience is the best teacher. Typically you want all the logical things - mages in the back, archers in front of them, main force in front of them and decoys/screens up close. But it all depends on what you can muster and what you fight. As Abysia for example you might want to put a number of mages up close as it helps thier accuracy in throwing fireballs and it allows them to use the killer fire spells (e.g. Fire Storm).

MP is the true test. IMHO the really really good players are very skilled at setting up thier battle troops/squads. Most of that knowledge is gained through hard won experience and play testing. I still sometimes feel like a complete newb when I watch my battle results...