Most of the activity in Seaquen is not terribly map-dependant. The players will probably spend their time between the north and south harbour, and the refugee camps. The many troubles seaquen needs help with, are more flavorful than tactical challanges - you can make tactical maps on the fly as needed.
For example I had the green dragon's lair as a small island in the middle of a ring-shaped lake, and I had the flaming rat swarm encounter take place in a resident's basement.
All of the (optional) encounters between Act 1 (the swamp) and act 4 (the theatre) are small and much more focused on HOW your players want to help, if they want to use diplomacy, sneak around, and such - it's not all about fighting and the big map for Seaquen's penninsula can show your players where they're walking to and from.
I recommend you let your players imagine the encounters with no maps until a fight *has* to break out and let them roll dice and say who they're talking to, or what they're doing with no mini's or maps
It's a lot of fun to just talk about play your characters and think about how to handle a situation without focusing too much on the tactical/positioning side of things too much

WotBS is a good mix of this kind of play, and heavy-handed combat with tactical choices. The dungeon crawl in act 5 is the oppisite way!