Both sides in an engage action will always roll 2d6 (picking the highest) regardless of how many formations were on each side.
This is because during an engage action all the formations, attacking or defending count as 1 formation until it is resolved.
From the Commander rule (needed to do a combined assault)
Highlighted the relevant parts.
Quote:
2.1.2 Commanders
Some units and characters are noted as being
commanders
.
Commanders can order up to three formations of troops to follow them when they make an assault, as long as all the formations have at least one unit within 5cm of a unit from the commander’s formation.
Make a single initiative roll for all the formations, counting a - 1 modifier if any have Blast markers. If the test is failed then the commander’s formation receives a Blast marker and must take a hold action, but the other formations are unaffected (and may take an action later in the turn).
If the test is passed then all three formations may take an engage action. Treat the three formations as if they were a single formation for all rules purposes for the duration of the assault. A 2D6 roll is used to resolve a combined assault. If the attackers lose then each formation is broken. If they win then each formation receives a number of Blast markers equal to the casualties it suffered in the combat
From the 1.12.10 Intermingled rules section
Quote:
SPECIAL RULE
1.12.10 Intermingled Formations
Occasionally an attacker will wish to attack a position where units from two enemy formations are intermingled together. When a player declares the target for a charging formation he can choose, if he wishes, to include any enemy formations that are intermingled with the target formation as being part of the target of the charge. Two formations are intermingled if they have any units within 5cm of each other.if there are two or more formations within 5cm of the target formation, then the attacker can choose to include one or more of them as the target, he does not though have to include any of them. For the purposes of the assault, the intermingled formation is treated as being a single formation. All of the intermingled formations are allowed to make counter charges, and hits may be allocated to all of the formations involved. Once casualties have been worked out, a 2D6 roll is used to resolve the assault. Add together all of the Blast markers on the intermingled formations when working out the result of the assault. If the defender loses then each formation is broken and must withdraw. If the defender wins then each formation receives a number of Blast markers equal to the number of casualties it suffered in the combat (ie, if one defending formation lost two units and then another one, then the first would get two Blast markers and theother would receive one Blast marker).
Hope this helps