Destroy All Humans! 2

Do not worry too much about completing all of the Arkvoodle quests in Bay City until:
1) You've completed Story Mission 5 (the finale of Bay City's story missions)
2) You've made it to Albion.

Once you've made it to Albion, complete all of the ones available to you in Bay City, then return to Albion and finish up to the 4th or 5th story mission. Now, when you're completing Arkvoodle missions in Albion, you'll actually have to return to Bay City to complete the last one, which requires you to recruit the Freak to paint flyers for you.