Question about WotG storyline.

So, in coming back to the game after a good 5+ year break, I'm curious about an aspect of WotG, i notice that the line for the missions actually goes something like Mission, Mission, City Quest, City Quest, Mission, etc.

Being OCD like I am, I'd like to complete all 3 city's storylines. How would I go about this? Do I complete all of WotG under San d'Oria, then back track and do it all again under Bastok? Or do i swap alliegence 3 times each time i come to a city quest within the mission line?

I know was probably a garbled mess, but any help would be appreciated. ^^.
Mainly I'd just like to be able to buy the atma's for finishing each cities past questline. Thanks.

The quests, are quests. You can do them at any time. completing just one specific story line (doesn't matter which) regardless of campaign allegiance is merely a requirement for the missions. As they are quests, it doesn't matter which series you do or how many of them.

Ah, so I could go through the entire WotG mission set, doing the San d'Orian quests when required, finish WotG. then go back and do only the quests for Bastok, followed by only the quests for Windurst, switching back to San d'Oria (cause I love Sandy). That doesn't sound so bad now that I think about it. Thanks.

You don't have to switch allegiance, they're quests. You can do them at any time (so long as you are allied to something, doesn't matter what).