Just got Hero's Call and they have a section in it that specifically mentions large scale combat. I believe it's called extended challenges.

Here are the currently final version of the rules I used to run my battle.

The Map
The battle is played out on a hexagonal grid map. Each space on the map is referred to as a "hex".

Units
Each Unit is represented by 1 Standup and a numbered Dice, known as a "Member Dice".

Member Dice
The Dice represents the Units current and maximum number of Members.
The type of Dice (D4, D6, D8 etc) varies based on the unit type.

Fortifications
Shown by an arrow pointing out from the fortified hex to one or more adjecent hexes.
Performing an an Attack Action directly against the arrows direction adds 1 Challange Dice.
Moving directly against the arrow demands an Average Athletics Check.

Buildings
Hexes with buildings in them can not be entered or occupied.

Trees
Hexes with trees grant +2 Defense to Ranged attacks.

Characters
A Unit may be led by a Character. If so, use the Characters standup to represent the unit.
Whenever a unit needs to use an Attribute or Skill, compare the Units and Characters stats. Use whichever is higher.
Units led by a Character uses the Characters Stance.

Monsters or single character
Monsters or Characters not part of a unit uses their THx2 Wounds amount, indicated in their stats.

Manouver
Each Unit may move 1 hex as a manouver.
Each Unit may pay 1 Wound to use additional manouvers.

Engagement
When a card or rule describes an Engagement, it refers to all hexes touching the hex of the relevant Unit/Monster/Character.

Disengaging
Moving away from an enemy Unit costs 1 Wound.

Flanking
If you attack a Unit in melee while an allied Unit is placed on one of the three hexes on the opposite side, you recieve 1 Expertice Dice to the attack check.

Action Cards
Units may only use the Basic Actions "Melee Strike" and "Ranged Shot". The GM may add additional actions he feels are appropriate.

Outnumbering
When attacking an enemy unit in melee, compare number of Members of the attacking and defending unit. If the "Attacker Members" > "Defender Members" the attackers recieves 1 Fortune Dice for each Member they exceeds the defenders.

Ranged Attacks
When attacking an enemy unit at range, count the number of members in the attacking unit and subtract 1. Add that many Fortune Dice.

Converting Dice
For every 4 Fortune Dice, remove these from the Dice Pool and add an Expertise Dice instead.

Range
Count the number of hexes, starting with the one in front of the attacking unit and ending with the target hex.
1: Engaged, 2: Close, 3: Normal, 4-5:Long, 6-8: Extreme range

Wounds
Each Member of a Unit has Wounds=TH.
When a Unit suffer Wounds, place a Fatigue/Stress token next to its Members Dice to indicate this.
When a Unit looses as many wounds as its TH, remove one Member and reset the Fatigue/Stress tokens.

Regaining Wounds
If the Unit regains Wounds, it can only heal Members that are injured. It can not regain fallen Members.

Fatigue/Stress
If a Unit should gain Fatigue/Stress, add that amount of Wounds.
If a Unit should loose Faitgue/Stress, remove that amount of Wounds.

Critical Wounds
If a Unit suffers a Critical Wound, it looses the Critical Rating amount of Members.
If a Monster/Character suffers a Critical Wound, apply it as normal.

Critically Wounded
If a Unit has half or less of its Members left, it is considered Critically Wounded.

Morale
If a Unit is reduced to half or less of its original Members, it must make a Normal Discipline or Leadership Check.
If the Unit fails the check, it recieves the Demoralised condition and looses as many members as Failures.

Demoralized Units
At the start of each turn, a Unit with the Demoralized effect must roll a Normal Discipline or Leadership test. If it fails, remove one Member for each Failure and move the unit one move away from any enemy units. Its turn then ends.
If it succeeds, remove the Demoralised condition.

0 Wounds/Members
If a Unit or Monster is reduced to 0 Wounds/Members, it is removed from the board.
If a Character is part of the Unit, he is knocked Unconcious until the end of the battle.

Turns
The GM decides the initiative order based on the situation.
The Inititive tracker simply consist of one turn for each side in the battle.
The players work together to move all their units.

very nice, gonna try that out tomorrow, i'll give you a report!

Some tips if you use this:

It's going to take at least a couple of hours to play, depending on the size of the armies and how familiar everyone is with the rules. I used it as a "Boss Fight" at the end of the first half of my campaign. I wouldn't use this for general combat.

Avoid having too big units. I'd say nothing bigger than a 10-man unit. Otherwise you'll end up with a lot of dice, which is part of the reason the "Converting Dice" rule is there.

It's implyed but never directly stated: I didn't use any defensive action cards. This is to cut down on the bookkeeping and increase the rate of fatalities.

thanks. i will also use it for a big boss fight at the end of our current adventure, at least parts of it since i don'T think there will be those many troops with the PCs

I've uploaded the rules as a word-file to rpggeek.com:

http://www.rpggeek.com/filepage/78576/large-scale-comat-in-wfrp