Its been a while since I read the rules and in the try out games I have played we opted not to do the 'front end' part of the game, to keep it simple while we learn the mechanics.
But from memory, the commanders get some options to play stratagems and scouting forces can be added to your force, these influence who gets first turn and how the army arrives. The armies are split into commands, so generally you have an advanced force, a main body, a rear guard and options for scouting and an outflanking force. When the various forces arrive is influenced by the scouting and stratagems.
In the example game in the rules the Crusaders get in a right mess! The Saracens all arrive together, with only the Crusaders advanced force to face them, then the Main body and rearguard get delayed and the crusaders outflanking force gets driven off fairly easily. It makes it a tough game for the Crusaders but they always seem to be in with a chance of winning the game (although they don't!)
With regard to army activation each command, advanced, main body, rearguard etc, has a card, at the start of the turn you choose which order these cards are in, so if you want your main body to go first you put that on the top of your deck. Both sides then determine initiative and the side that is going first reveals their top card and moves that command then their opponent reveals their top card and moves that command. This means you are prioritising your army each turn and trying to second guess your enemy. In the example game another reason the Saracens win in my opinion, is because they out think the Crusaders in this part of the game.
The other part of the command syatem is that often the commander in charge of a force can't activated all his units, once all the commands have been, in the card order part of the turn, then the un-activated units all go at the end, so again there is a prioritising exercise going on within each command.
The reason I like all this is there is plenty to think about as a commander and its ideal for multi-player games.
Hope that helps.