In the past I've played a simplified style of campaign, where we played the scenarios in chronological order, and kept a running tally of banners scored.
The only balance provision we used was where there was a difference in the Command Cards each player had, then the player with the least Command Cards got bonus banners equivalent to the difference.
For a long example of the entire Peninsular campaign, see
www.boardgamegeek.com/blog/2535/peninsular-campaign
Using those rules the scores were
301 Wertingen (8 October 1805) French: 5 Austrian: 3
302 Günzburg (9 October 1805) French: 7 Austrian: 3
303 Haslach-Jungingen (11 October 1805) French: 6 Austrian: 6
304 Elchingen (14 October 1805) French: 7 Austrian: 4
TOTAL French: 25 Austrian: 16